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3eiy.cif
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3eiy.cif
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data_3EIY
#
_entry.id 3EIY
#
_audit_conform.dict_name mmcif_pdbx.dic
_audit_conform.dict_version 5.281
_audit_conform.dict_location http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
#
loop_
_database_2.database_id
_database_2.database_code
PDB 3EIY
RCSB RCSB049380
WWPDB D_1000049380
#
loop_
_pdbx_database_related.db_name
_pdbx_database_related.db_id
_pdbx_database_related.details
_pdbx_database_related.content_type
TargetDB BupsA.00023.a . unspecified
PDB 3d63
;The same protein, "open" conformation, apo form, in space group P21212
;
unspecified
PDB 3EIZ . unspecified
PDB 3EJ0 . unspecified
PDB 3EJ2 . unspecified
#
_pdbx_database_status.status_code REL
_pdbx_database_status.entry_id 3EIY
_pdbx_database_status.recvd_initial_deposition_date 2008-09-17
_pdbx_database_status.deposit_site RCSB
_pdbx_database_status.process_site RCSB
_pdbx_database_status.status_code_sf REL
_pdbx_database_status.status_code_mr ?
_pdbx_database_status.SG_entry Y
_pdbx_database_status.status_code_cs ?
_pdbx_database_status.pdb_format_compatible Y
#
_audit_author.name 'Seattle Structural Genomics Center for Infectious Disease (SSGCID)'
_audit_author.pdbx_ordinal 1
#
loop_
_citation.id
_citation.title
_citation.journal_abbrev
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.year
_citation.journal_id_ASTM
_citation.country
_citation.journal_id_ISSN
_citation.journal_id_CSD
_citation.book_publisher
_citation.pdbx_database_id_PubMed
_citation.pdbx_database_id_DOI
primary 'The role of medical structural genomics in discovering new drugs for infectious diseases.' 'PLoS Comput Biol' 5
e1000530 e1000530 2009 ? US 1553-734X 0353 ? 19855826 10.1371/journal.pcbi.1000530
1 'Combining functional and structural genomics to sample the essential Burkholderia structome.' 'Plos One' 8 e53851
e53851 2013 ? US 1932-6203 ? ? 23382856 10.1371/journal.pone.0053851
#
loop_
_citation_author.citation_id
_citation_author.name
_citation_author.ordinal
primary 'Van Voorhis, W.C.' 1
primary 'Hol, W.G.' 2
primary 'Myler, P.J.' 3
primary 'Stewart, L.J.' 4
1 'Baugh, L.' 5
1 'Gallagher, L.A.' 6
1 'Patrapuvich, R.' 7
1 'Clifton, M.C.' 8
1 'Gardberg, A.S.' 9
1 'Edwards, T.E.' 10
1 'Armour, B.' 11
1 'Begley, D.W.' 12
1 'Dieterich, S.H.' 13
1 'Dranow, D.M.' 14
1 'Abendroth, J.' 15
1 'Fairman, J.W.' 16
1 'Fox, D.' 17
1 'Staker, B.L.' 18
1 'Phan, I.' 19
1 'Gillespie, A.' 20
1 'Choi, R.' 21
1 'Nakazawa-Hewitt, S.' 22
1 'Nguyen, M.T.' 23
1 'Napuli, A.' 24
1 'Barrett, L.' 25
1 'Buchko, G.W.' 26
1 'Stacy, R.' 27
1 'Myler, P.J.' 28
1 'Stewart, L.J.' 29
1 'Manoil, C.' 30
1 'Van Voorhis, W.C.' 31
#
_cell.entry_id 3EIY
_cell.length_a 100.952
_cell.length_b 100.952
_cell.length_c 111.233
_cell.angle_alpha 90.00
_cell.angle_beta 90.00
_cell.angle_gamma 120.00
_cell.Z_PDB 12
_cell.pdbx_unique_axis ?
_cell.length_a_esd ?
_cell.length_b_esd ?
_cell.length_c_esd ?
_cell.angle_alpha_esd ?
_cell.angle_beta_esd ?
_cell.angle_gamma_esd ?
#
_symmetry.entry_id 3EIY
_symmetry.space_group_name_H-M 'P 63 2 2'
_symmetry.pdbx_full_space_group_name_H-M ?
_symmetry.cell_setting ?
_symmetry.Int_Tables_number 182
_symmetry.space_group_name_Hall ?
#
loop_
_entity.id
_entity.type
_entity.src_method
_entity.pdbx_description
_entity.formula_weight
_entity.pdbx_number_of_molecules
_entity.pdbx_ec
_entity.pdbx_mutation
_entity.pdbx_fragment
_entity.details
1 polymer man 'Inorganic pyrophosphatase' 21473.625 1 3.6.1.1 ? ? ?
2 non-polymer syn 'POTASSIUM ION' 39.098 1 ? ? ? ?
3 non-polymer syn 'SODIUM ION' 22.990 2 ? ? ? ?
4 non-polymer syn 'PYROPHOSPHATE 2-' 175.959 1 ? ? ? ?
5 non-polymer syn 'TETRAETHYLENE GLYCOL' 194.226 1 ? ? ? ?
6 non-polymer syn 'DI(HYDROXYETHYL)ETHER' 106.120 2 ? ? ? ?
7 water nat water 18.015 112 ? ? ? ?
#
_entity_poly.entity_id 1
_entity_poly.type 'polypeptide(L)'
_entity_poly.nstd_linkage no
_entity_poly.nstd_monomer no
_entity_poly.pdbx_seq_one_letter_code
;MAHHHHHHMGTLEAQTQGPGSMSFSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFI
PQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFF
EQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK
;
_entity_poly.pdbx_seq_one_letter_code_can
;MAHHHHHHMGTLEAQTQGPGSMSFSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFI
PQTLSGDGDPVDVLVITPFPLLAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFF
EQYKALEKGKWVKVEGWDGIDAAHKEITDGVANFKK
;
_entity_poly.pdbx_strand_id A
_entity_poly.pdbx_target_identifier BupsA.00023.a
#
loop_
_entity_poly_seq.entity_id
_entity_poly_seq.num
_entity_poly_seq.mon_id
_entity_poly_seq.hetero
1 1 MET n
1 2 ALA n
1 3 HIS n
1 4 HIS n
1 5 HIS n
1 6 HIS n
1 7 HIS n
1 8 HIS n
1 9 MET n
1 10 GLY n
1 11 THR n
1 12 LEU n
1 13 GLU n
1 14 ALA n
1 15 GLN n
1 16 THR n
1 17 GLN n
1 18 GLY n
1 19 PRO n
1 20 GLY n
1 21 SER n
1 22 MET n
1 23 SER n
1 24 PHE n
1 25 SER n
1 26 ASN n
1 27 VAL n
1 28 PRO n
1 29 ALA n
1 30 GLY n
1 31 LYS n
1 32 ASP n
1 33 LEU n
1 34 PRO n
1 35 GLN n
1 36 ASP n
1 37 PHE n
1 38 ASN n
1 39 VAL n
1 40 ILE n
1 41 ILE n
1 42 GLU n
1 43 ILE n
1 44 PRO n
1 45 ALA n
1 46 GLN n
1 47 SER n
1 48 GLU n
1 49 PRO n
1 50 VAL n
1 51 LYS n
1 52 TYR n
1 53 GLU n
1 54 ALA n
1 55 ASP n
1 56 LYS n
1 57 ALA n
1 58 LEU n
1 59 GLY n
1 60 LEU n
1 61 LEU n
1 62 VAL n
1 63 VAL n
1 64 ASP n
1 65 ARG n
1 66 PHE n
1 67 ILE n
1 68 GLY n
1 69 THR n
1 70 GLY n
1 71 MET n
1 72 ARG n
1 73 TYR n
1 74 PRO n
1 75 VAL n
1 76 ASN n
1 77 TYR n
1 78 GLY n
1 79 PHE n
1 80 ILE n
1 81 PRO n
1 82 GLN n
1 83 THR n
1 84 LEU n
1 85 SER n
1 86 GLY n
1 87 ASP n
1 88 GLY n
1 89 ASP n
1 90 PRO n
1 91 VAL n
1 92 ASP n
1 93 VAL n
1 94 LEU n
1 95 VAL n
1 96 ILE n
1 97 THR n
1 98 PRO n
1 99 PHE n
1 100 PRO n
1 101 LEU n
1 102 LEU n
1 103 ALA n
1 104 GLY n
1 105 SER n
1 106 VAL n
1 107 VAL n
1 108 ARG n
1 109 ALA n
1 110 ARG n
1 111 ALA n
1 112 LEU n
1 113 GLY n
1 114 MET n
1 115 LEU n
1 116 LYS n
1 117 MET n
1 118 THR n
1 119 ASP n
1 120 GLU n
1 121 SER n
1 122 GLY n
1 123 VAL n
1 124 ASP n
1 125 ALA n
1 126 LYS n
1 127 LEU n
1 128 VAL n
1 129 ALA n
1 130 VAL n
1 131 PRO n
1 132 HIS n
1 133 ASP n
1 134 LYS n
1 135 VAL n
1 136 CYS n
1 137 PRO n
1 138 MET n
1 139 THR n
1 140 ALA n
1 141 ASN n
1 142 LEU n
1 143 LYS n
1 144 SER n
1 145 ILE n
1 146 ASP n
1 147 ASP n
1 148 VAL n
1 149 PRO n
1 150 ALA n
1 151 TYR n
1 152 LEU n
1 153 LYS n
1 154 ASP n
1 155 GLN n
1 156 ILE n
1 157 LYS n
1 158 HIS n
1 159 PHE n
1 160 PHE n
1 161 GLU n
1 162 GLN n
1 163 TYR n
1 164 LYS n
1 165 ALA n
1 166 LEU n
1 167 GLU n
1 168 LYS n
1 169 GLY n
1 170 LYS n
1 171 TRP n
1 172 VAL n
1 173 LYS n
1 174 VAL n
1 175 GLU n
1 176 GLY n
1 177 TRP n
1 178 ASP n
1 179 GLY n
1 180 ILE n
1 181 ASP n
1 182 ALA n
1 183 ALA n
1 184 HIS n
1 185 LYS n
1 186 GLU n
1 187 ILE n
1 188 THR n
1 189 ASP n
1 190 GLY n
1 191 VAL n
1 192 ALA n
1 193 ASN n
1 194 PHE n
1 195 LYS n
1 196 LYS n
#
_entity_src_gen.entity_id 1
_entity_src_gen.pdbx_src_id 1
_entity_src_gen.pdbx_alt_source_flag sample
_entity_src_gen.pdbx_seq_type ?
_entity_src_gen.pdbx_beg_seq_num ?
_entity_src_gen.pdbx_end_seq_num ?
_entity_src_gen.gene_src_common_name ?
_entity_src_gen.gene_src_genus ?
_entity_src_gen.pdbx_gene_src_gene 'ppa, BURPS1710b_1237'
_entity_src_gen.gene_src_species ?
_entity_src_gen.gene_src_strain ?
_entity_src_gen.gene_src_tissue ?
_entity_src_gen.gene_src_tissue_fraction ?
_entity_src_gen.gene_src_details ?
_entity_src_gen.pdbx_gene_src_fragment ?
_entity_src_gen.pdbx_gene_src_scientific_name 'Burkholderia pseudomallei 1710b'
_entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id 320372
_entity_src_gen.pdbx_gene_src_variant ?
_entity_src_gen.pdbx_gene_src_cell_line ?
_entity_src_gen.pdbx_gene_src_atcc ?
_entity_src_gen.pdbx_gene_src_organ ?
_entity_src_gen.pdbx_gene_src_organelle ?
_entity_src_gen.pdbx_gene_src_cell ?
_entity_src_gen.pdbx_gene_src_cellular_location ?
_entity_src_gen.host_org_common_name ?
_entity_src_gen.pdbx_host_org_scientific_name 'Escherichia coli'
_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id 562
_entity_src_gen.host_org_genus ?
_entity_src_gen.pdbx_host_org_gene ?
_entity_src_gen.pdbx_host_org_organ ?
_entity_src_gen.host_org_species ?
_entity_src_gen.pdbx_host_org_tissue ?
_entity_src_gen.pdbx_host_org_tissue_fraction ?
_entity_src_gen.pdbx_host_org_strain 'BL21(DE3)'
_entity_src_gen.pdbx_host_org_variant ?
_entity_src_gen.pdbx_host_org_cell_line ?
_entity_src_gen.pdbx_host_org_atcc ?
_entity_src_gen.pdbx_host_org_culture_collection ?
_entity_src_gen.pdbx_host_org_cell ?
_entity_src_gen.pdbx_host_org_organelle ?
_entity_src_gen.pdbx_host_org_cellular_location ?
_entity_src_gen.pdbx_host_org_vector_type Plasmid
_entity_src_gen.pdbx_host_org_vector ?
_entity_src_gen.host_org_details ?
_entity_src_gen.expression_system_id ?
_entity_src_gen.plasmid_name AVA0421
_entity_src_gen.plasmid_details ?
_entity_src_gen.pdbx_description ?
#
_struct_ref.id 1
_struct_ref.db_name UNP
_struct_ref.db_code Q3JUV5_BURP1
_struct_ref.pdbx_db_accession Q3JUV5
_struct_ref.entity_id 1
_struct_ref.pdbx_seq_one_letter_code
;MSFSNVPAGKDLPQDFNVIIEIPAQSEPVKYEADKALGLLVVDRFIGTGMRYPVNYGFIPQTLSGDGDPVDVLVITPFPL
LAGSVVRARALGMLKMTDESGVDAKLVAVPHDKVCPMTANLKSIDDVPAYLKDQIKHFFEQYKALEKGKWVKVEGWDGID
AAHKEITDGVANFKK
;
_struct_ref.pdbx_align_begin 1
_struct_ref.pdbx_db_isoform ?
#
_struct_ref_seq.align_id 1
_struct_ref_seq.ref_id 1
_struct_ref_seq.pdbx_PDB_id_code 3EIY
_struct_ref_seq.pdbx_strand_id A
_struct_ref_seq.seq_align_beg 22
_struct_ref_seq.pdbx_seq_align_beg_ins_code ?
_struct_ref_seq.seq_align_end 196
_struct_ref_seq.pdbx_seq_align_end_ins_code ?
_struct_ref_seq.pdbx_db_accession Q3JUV5
_struct_ref_seq.db_align_beg 1
_struct_ref_seq.pdbx_db_align_beg_ins_code ?
_struct_ref_seq.db_align_end 175
_struct_ref_seq.pdbx_db_align_end_ins_code ?
_struct_ref_seq.pdbx_auth_seq_align_beg 1
_struct_ref_seq.pdbx_auth_seq_align_end 175
#
loop_
_struct_ref_seq_dif.align_id
_struct_ref_seq_dif.pdbx_pdb_id_code
_struct_ref_seq_dif.mon_id
_struct_ref_seq_dif.pdbx_pdb_strand_id
_struct_ref_seq_dif.seq_num
_struct_ref_seq_dif.pdbx_pdb_ins_code
_struct_ref_seq_dif.pdbx_seq_db_name
_struct_ref_seq_dif.pdbx_seq_db_accession_code
_struct_ref_seq_dif.db_mon_id
_struct_ref_seq_dif.pdbx_seq_db_seq_num
_struct_ref_seq_dif.details
_struct_ref_seq_dif.pdbx_auth_seq_num
_struct_ref_seq_dif.pdbx_ordinal
1 3EIY MET A 1 ? UNP Q3JUV5 ? ? 'expression tag' -20 1
1 3EIY ALA A 2 ? UNP Q3JUV5 ? ? 'expression tag' -19 2
1 3EIY HIS A 3 ? UNP Q3JUV5 ? ? 'expression tag' -18 3
1 3EIY HIS A 4 ? UNP Q3JUV5 ? ? 'expression tag' -17 4
1 3EIY HIS A 5 ? UNP Q3JUV5 ? ? 'expression tag' -16 5
1 3EIY HIS A 6 ? UNP Q3JUV5 ? ? 'expression tag' -15 6
1 3EIY HIS A 7 ? UNP Q3JUV5 ? ? 'expression tag' -14 7
1 3EIY HIS A 8 ? UNP Q3JUV5 ? ? 'expression tag' -13 8
1 3EIY MET A 9 ? UNP Q3JUV5 ? ? 'expression tag' -12 9
1 3EIY GLY A 10 ? UNP Q3JUV5 ? ? 'expression tag' -11 10
1 3EIY THR A 11 ? UNP Q3JUV5 ? ? 'expression tag' -10 11
1 3EIY LEU A 12 ? UNP Q3JUV5 ? ? 'expression tag' -9 12
1 3EIY GLU A 13 ? UNP Q3JUV5 ? ? 'expression tag' -8 13
1 3EIY ALA A 14 ? UNP Q3JUV5 ? ? 'expression tag' -7 14
1 3EIY GLN A 15 ? UNP Q3JUV5 ? ? 'expression tag' -6 15
1 3EIY THR A 16 ? UNP Q3JUV5 ? ? 'expression tag' -5 16
1 3EIY GLN A 17 ? UNP Q3JUV5 ? ? 'expression tag' -4 17
1 3EIY GLY A 18 ? UNP Q3JUV5 ? ? 'expression tag' -3 18
1 3EIY PRO A 19 ? UNP Q3JUV5 ? ? 'expression tag' -2 19
1 3EIY GLY A 20 ? UNP Q3JUV5 ? ? 'expression tag' -1 20
1 3EIY SER A 21 ? UNP Q3JUV5 ? ? 'expression tag' 0 21
#
loop_
_chem_comp.id
_chem_comp.type
_chem_comp.mon_nstd_flag
_chem_comp.name
_chem_comp.pdbx_synonyms
_chem_comp.formula
_chem_comp.formula_weight
ALA 'L-peptide linking' y ALANINE ? 'C3 H7 N O2' 89.093
ARG 'L-peptide linking' y ARGININE ? 'C6 H15 N4 O2 1' 175.209
ASN 'L-peptide linking' y ASPARAGINE ? 'C4 H8 N2 O3' 132.118
ASP 'L-peptide linking' y 'ASPARTIC ACID' ? 'C4 H7 N O4' 133.103
CYS 'L-peptide linking' y CYSTEINE ? 'C3 H7 N O2 S' 121.158
GLN 'L-peptide linking' y GLUTAMINE ? 'C5 H10 N2 O3' 146.144
GLU 'L-peptide linking' y 'GLUTAMIC ACID' ? 'C5 H9 N O4' 147.129
GLY 'peptide linking' y GLYCINE ? 'C2 H5 N O2' 75.067
HIS 'L-peptide linking' y HISTIDINE ? 'C6 H10 N3 O2 1' 156.162
HOH non-polymer . WATER ? 'H2 O' 18.015
ILE 'L-peptide linking' y ISOLEUCINE ? 'C6 H13 N O2' 131.173
K non-polymer . 'POTASSIUM ION' ? 'K 1' 39.098
LEU 'L-peptide linking' y LEUCINE ? 'C6 H13 N O2' 131.173
LYS 'L-peptide linking' y LYSINE ? 'C6 H15 N2 O2 1' 147.195
MET 'L-peptide linking' y METHIONINE ? 'C5 H11 N O2 S' 149.211
NA non-polymer . 'SODIUM ION' ? 'Na 1' 22.990
PEG non-polymer . 'DI(HYDROXYETHYL)ETHER' ? 'C4 H10 O3' 106.120
PG4 non-polymer . 'TETRAETHYLENE GLYCOL' ? 'C8 H18 O5' 194.226
PHE 'L-peptide linking' y PHENYLALANINE ? 'C9 H11 N O2' 165.189
POP non-polymer . 'PYROPHOSPHATE 2-' ? 'H2 O7 P2 -2' 175.959
PRO 'L-peptide linking' y PROLINE ? 'C5 H9 N O2' 115.130
SER 'L-peptide linking' y SERINE ? 'C3 H7 N O3' 105.093
THR 'L-peptide linking' y THREONINE ? 'C4 H9 N O3' 119.119
TRP 'L-peptide linking' y TRYPTOPHAN ? 'C11 H12 N2 O2' 204.225
TYR 'L-peptide linking' y TYROSINE ? 'C9 H11 N O3' 181.189
VAL 'L-peptide linking' y VALINE ? 'C5 H11 N O2' 117.146
#
_exptl.entry_id 3EIY
_exptl.method 'X-RAY DIFFRACTION'
_exptl.crystals_number 1
#
_exptl_crystal.id 1
_exptl_crystal.density_meas ?
_exptl_crystal.density_Matthews 3.81
_exptl_crystal.density_percent_sol 67.71
_exptl_crystal.description ?
_exptl_crystal.F_000 ?
_exptl_crystal.preparation ?
#
_exptl_crystal_grow.crystal_id 1
_exptl_crystal_grow.method 'VAPOR DIFFUSION, SITTING DROP'
_exptl_crystal_grow.temp 289
_exptl_crystal_grow.temp_details ?
_exptl_crystal_grow.pH 6.30
_exptl_crystal_grow.pdbx_details
'100 MM NA/K PHOSPHATE, PH 6.3, 49.5% PEG 200. CRYSTAL 3 MONTHS OLD., pH 6.30, VAPOR DIFFUSION, SITTING DROP, temperature 289K'
_exptl_crystal_grow.pdbx_pH_range ?
#
_diffrn.id 1
_diffrn.ambient_temp 100.0
_diffrn.ambient_temp_details ?
_diffrn.crystal_id 1
#
_diffrn_detector.diffrn_id 1
_diffrn_detector.detector CCD
_diffrn_detector.type 'RIGAKU SATURN 944'
_diffrn_detector.pdbx_collection_date 2008-09-04
_diffrn_detector.details ?
#
_diffrn_radiation.diffrn_id 1
_diffrn_radiation.wavelength_id 1
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l M
_diffrn_radiation.monochromator ?
_diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH'
_diffrn_radiation.pdbx_scattering_type x-ray
#
_diffrn_radiation_wavelength.id 1
_diffrn_radiation_wavelength.wavelength 1.5418
_diffrn_radiation_wavelength.wt 1.0
#
_diffrn_source.diffrn_id 1
_diffrn_source.source 'ROTATING ANODE'
_diffrn_source.type 'RIGAKU MICROMAX-007 HF'
_diffrn_source.pdbx_synchrotron_site ?
_diffrn_source.pdbx_synchrotron_beamline ?
_diffrn_source.pdbx_wavelength ?
_diffrn_source.pdbx_wavelength_list 1.5418
#
_reflns.entry_id 3EIY
_reflns.observed_criterion_sigma_I ?
_reflns.observed_criterion_sigma_F ?
_reflns.d_resolution_low 50.000
_reflns.d_resolution_high 2.100
_reflns.number_obs 19792
_reflns.number_all ?
_reflns.percent_possible_obs 98.7
_reflns.pdbx_Rmerge_I_obs 0.10300
_reflns.pdbx_Rsym_value ?
_reflns.pdbx_netI_over_sigmaI 8.9000
_reflns.B_iso_Wilson_estimate ?
_reflns.pdbx_redundancy 3.600
_reflns.R_free_details ?
_reflns.limit_h_max ?
_reflns.limit_h_min ?
_reflns.limit_k_max ?
_reflns.limit_k_min ?
_reflns.limit_l_max ?
_reflns.limit_l_min ?
_reflns.observed_criterion_F_max ?
_reflns.observed_criterion_F_min ?
_reflns.pdbx_chi_squared ?
_reflns.pdbx_scaling_rejects ?
_reflns.pdbx_ordinal 1
_reflns.pdbx_diffrn_id 1
#
_reflns_shell.d_res_high 2.10
_reflns_shell.d_res_low 2.18
_reflns_shell.percent_possible_all 98.5
_reflns_shell.Rmerge_I_obs 0.66900
_reflns_shell.pdbx_Rsym_value ?
_reflns_shell.meanI_over_sigI_obs ?
_reflns_shell.pdbx_redundancy 2.70
_reflns_shell.percent_possible_obs ?
_reflns_shell.number_unique_all ?
_reflns_shell.number_measured_all ?
_reflns_shell.number_measured_obs ?
_reflns_shell.number_unique_obs ?
_reflns_shell.pdbx_chi_squared ?
_reflns_shell.pdbx_ordinal 1
_reflns_shell.pdbx_diffrn_id 1
#
_refine.entry_id 3EIY
_refine.ls_number_reflns_obs 19547
_refine.ls_number_reflns_all ?
_refine.pdbx_ls_sigma_I ?
_refine.pdbx_ls_sigma_F 0.000
_refine.pdbx_data_cutoff_high_absF ?
_refine.pdbx_data_cutoff_low_absF ?
_refine.pdbx_data_cutoff_high_rms_absF ?
_refine.ls_d_res_low 50.000
_refine.ls_d_res_high 2.10
_refine.ls_percent_reflns_obs ?
_refine.ls_R_factor_obs 0.213
_refine.ls_R_factor_all ?
_refine.ls_R_factor_R_work 0.211
_refine.ls_R_factor_R_free 0.249
_refine.ls_R_factor_R_free_error ?
_refine.ls_R_factor_R_free_error_details ?
_refine.ls_percent_reflns_R_free 5.100
_refine.ls_number_reflns_R_free 991
_refine.ls_number_parameters ?
_refine.ls_number_restraints ?
_refine.occupancy_min ?
_refine.occupancy_max ?
_refine.correlation_coeff_Fo_to_Fc 0.948
_refine.correlation_coeff_Fo_to_Fc_free 0.929
_refine.B_iso_mean 30.12
_refine.aniso_B[1][1] 0.80000
_refine.aniso_B[2][2] 0.80000
_refine.aniso_B[3][3] -1.21000
_refine.aniso_B[1][2] 0.40000
_refine.aniso_B[1][3] 0.00000
_refine.aniso_B[2][3] 0.00000
_refine.solvent_model_details MASK
_refine.solvent_model_param_ksol ?
_refine.solvent_model_param_bsol ?
_refine.pdbx_solvent_vdw_probe_radii 1.20
_refine.pdbx_solvent_ion_probe_radii 0.80
_refine.pdbx_solvent_shrinkage_radii 0.80
_refine.pdbx_ls_cross_valid_method THROUGHOUT
_refine.details 'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS'
_refine.pdbx_starting_model ?
_refine.pdbx_method_to_determine_struct 'MOLECULAR REPLACEMENT'
_refine.pdbx_isotropic_thermal_model ?
_refine.pdbx_stereochemistry_target_values 'MAXIMUM LIKELIHOOD'
_refine.pdbx_stereochem_target_val_spec_case ?
_refine.pdbx_R_Free_selection_details RANDOM
_refine.pdbx_overall_ESU_R 0.156
_refine.pdbx_overall_ESU_R_Free 0.152
_refine.overall_SU_ML 0.110
_refine.overall_SU_B 4.164
_refine.ls_redundancy_reflns_obs ?
_refine.B_iso_min ?
_refine.B_iso_max ?
_refine.overall_SU_R_Cruickshank_DPI ?
_refine.overall_SU_R_free ?
_refine.ls_wR_factor_R_free ?
_refine.ls_wR_factor_R_work ?
_refine.overall_FOM_free_R_set ?
_refine.overall_FOM_work_R_set ?
_refine.pdbx_overall_phase_error ?
_refine.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine.pdbx_diffrn_id 1
_refine.pdbx_TLS_residual_ADP_flag ?
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI ?
_refine.pdbx_overall_SU_R_Blow_DPI ?
_refine.pdbx_overall_SU_R_free_Blow_DPI ?
#
_refine_hist.pdbx_refine_id 'X-RAY DIFFRACTION'
_refine_hist.cycle_id LAST
_refine_hist.pdbx_number_atoms_protein 1330
_refine_hist.pdbx_number_atoms_nucleic_acid 0
_refine_hist.pdbx_number_atoms_ligand 39
_refine_hist.number_atoms_solvent 112
_refine_hist.number_atoms_total 1481
_refine_hist.d_res_high 2.10
_refine_hist.d_res_low 50.000
#
loop_
_refine_ls_restr.type
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
_refine_ls_restr.weight
_refine_ls_restr.number
_refine_ls_restr.pdbx_refine_id
_refine_ls_restr.pdbx_restraint_function
r_bond_refined_d 0.015 0.022 ? 1393 'X-RAY DIFFRACTION' ?
r_angle_refined_deg 1.460 1.994 ? 1886 'X-RAY DIFFRACTION' ?
r_dihedral_angle_1_deg 5.857 5.000 ? 173 'X-RAY DIFFRACTION' ?
r_dihedral_angle_2_deg 32.570 25.357 ? 56 'X-RAY DIFFRACTION' ?
r_dihedral_angle_3_deg 15.203 15.000 ? 222 'X-RAY DIFFRACTION' ?
r_dihedral_angle_4_deg 18.890 15.000 ? 4 'X-RAY DIFFRACTION' ?
r_chiral_restr 0.092 0.200 ? 209 'X-RAY DIFFRACTION' ?
r_gen_planes_refined 0.007 0.021 ? 1034 'X-RAY DIFFRACTION' ?
r_mcbond_it 0.890 1.500 ? 870 'X-RAY DIFFRACTION' ?
r_mcangle_it 1.604 2.000 ? 1408 'X-RAY DIFFRACTION' ?
r_scbond_it 2.198 3.000 ? 523 'X-RAY DIFFRACTION' ?
r_scangle_it 3.551 4.500 ? 478 'X-RAY DIFFRACTION' ?
#
_refine_ls_shell.pdbx_total_number_of_bins_used 20
_refine_ls_shell.d_res_high 2.10
_refine_ls_shell.d_res_low 2.15
_refine_ls_shell.number_reflns_R_work 1250
_refine_ls_shell.R_factor_R_work 0.3090
_refine_ls_shell.percent_reflns_obs 90.60
_refine_ls_shell.R_factor_R_free 0.4070
_refine_ls_shell.R_factor_R_free_error ?
_refine_ls_shell.percent_reflns_R_free ?
_refine_ls_shell.number_reflns_R_free 71
_refine_ls_shell.number_reflns_all ?
_refine_ls_shell.R_factor_all ?
_refine_ls_shell.number_reflns_obs ?
_refine_ls_shell.redundancy_reflns_obs ?
_refine_ls_shell.pdbx_refine_id 'X-RAY DIFFRACTION'
#
_struct.entry_id 3EIY
_struct.title
'Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound pyrophosphate'
_struct.pdbx_descriptor 'Inorganic pyrophosphatase (E.C.3.6.1.1)'
_struct.pdbx_model_details ?
_struct.pdbx_CASP_flag ?
_struct.pdbx_model_type_details ?
#
_struct_keywords.entry_id 3EIY
_struct_keywords.pdbx_keywords HYDROLASE
_struct_keywords.text
;structural genomics, SSGCID, pyrophosphatase, Hydrolase, BupsA.00023.a, Seattle Structural Genomics Center for Infectious Disease'
;
#
loop_
_struct_asym.id
_struct_asym.pdbx_blank_PDB_chainid_flag
_struct_asym.pdbx_modified
_struct_asym.entity_id
_struct_asym.details
A N N 1 ?
B N N 2 ?
C N N 3 ?
D N N 3 ?
E N N 4 ?
F N N 5 ?
G N N 6 ?
H N N 6 ?
I N N 7 ?
#
_struct_biol.id 1
#
loop_
_struct_conf.conf_type_id
_struct_conf.id
_struct_conf.pdbx_PDB_helix_id
_struct_conf.beg_label_comp_id
_struct_conf.beg_label_asym_id
_struct_conf.beg_label_seq_id
_struct_conf.pdbx_beg_PDB_ins_code
_struct_conf.end_label_comp_id
_struct_conf.end_label_asym_id
_struct_conf.end_label_seq_id
_struct_conf.pdbx_end_PDB_ins_code
_struct_conf.beg_auth_comp_id
_struct_conf.beg_auth_asym_id
_struct_conf.beg_auth_seq_id
_struct_conf.end_auth_comp_id
_struct_conf.end_auth_asym_id
_struct_conf.end_auth_seq_id
_struct_conf.pdbx_PDB_helix_class
_struct_conf.details
_struct_conf.pdbx_PDB_helix_length
HELX_P HELX_P1 1 SER A 23 ? VAL A 27 ? SER A 2 VAL A 6 5 ? 5
HELX_P HELX_P2 2 CYS A 136 ? ALA A 140 ? CYS A 115 ALA A 119 5 ? 5
HELX_P HELX_P3 3 SER A 144 ? VAL A 148 ? SER A 123 VAL A 127 5 ? 5
HELX_P HELX_P4 4 PRO A 149 ? TYR A 163 ? PRO A 128 TYR A 142 1 ? 15
HELX_P HELX_P5 5 GLY A 179 ? LYS A 196 ? GLY A 158 LYS A 175 1 ? 18
#
_struct_conf_type.id HELX_P
_struct_conf_type.criteria ?
_struct_conf_type.reference ?
#
loop_
_struct_conn.id
_struct_conn.conn_type_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_PDB_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.pdbx_ptnr1_PDB_ins_code
_struct_conn.pdbx_ptnr1_standard_comp_id
_struct_conn.ptnr1_symmetry
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.pdbx_ptnr2_label_alt_id
_struct_conn.pdbx_ptnr2_PDB_ins_code
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr2_auth_asym_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_symmetry
_struct_conn.pdbx_ptnr3_label_atom_id
_struct_conn.pdbx_ptnr3_label_seq_id
_struct_conn.pdbx_ptnr3_label_comp_id
_struct_conn.pdbx_ptnr3_label_asym_id
_struct_conn.pdbx_ptnr3_label_alt_id
_struct_conn.pdbx_ptnr3_PDB_ins_code
_struct_conn.details
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_value_order
metalc1 metalc ? ? A ASP 32 OD1 ? ? ? 1_555 B K . K ? ? A ASP 11 A K 176 1_555 ? ? ? ? ? ? ? 2.731 ?
metalc2 metalc ? ? A LEU 33 O ? ? ? 1_555 B K . K ? ? A LEU 12 A K 176 1_555 ? ? ? ? ? ? ? 2.650 ?
metalc3 metalc ? ? A GLN 35 OE1 ? ? ? 1_555 B K . K ? ? A GLN 14 A K 176 1_555 ? ? ? ? ? ? ? 2.922 ?
metalc4 metalc ? ? A ASP 92 OD2 ? ? ? 1_555 D NA . NA ? ? A ASP 71 A NA 178 1_555 ? ? ? ? ? ? ? 2.808 ?
metalc5 metalc ? ? A ASP 119 OD2 ? ? ? 1_555 C NA . NA ? ? A ASP 98 A NA 177 1_555 ? ? ? ? ? ? ? 2.646 ?
metalc6 metalc ? ? A ASP 124 OD1 ? ? ? 1_555 D NA . NA ? ? A ASP 103 A NA 178 1_555 ? ? ? ? ? ? ? 2.529 ?
metalc7 metalc ? ? A ASP 124 OD2 ? ? ? 1_555 C NA . NA ? ? A ASP 103 A NA 177 1_555 ? ? ? ? ? ? ? 2.577 ?
metalc8 metalc ? ? A ALA 125 O ? ? ? 1_555 D NA . NA ? ? A ALA 104 A NA 178 1_555 ? ? ? ? ? ? ? 2.919 ?
metalc9 metalc ? ? C NA . NA ? ? ? 1_555 E POP . O6 ? ? A NA 177 A POP 179 1_555 ? ? ? ? ? ? ? 2.560 ?
metalc10 metalc ? ? C NA . NA ? ? ? 1_555 I HOH . O ? ? A NA 177 A HOH 257 1_555 ? ? ? ? ? ? ? 2.654 ?
metalc11 metalc ? ? C NA . NA ? ? ? 1_555 E POP . O3 ? ? A NA 177 A POP 179 1_555 ? ? ? ? ? ? ? 2.204 ?
metalc12 metalc ? ? C NA . NA ? ? ? 1_555 I HOH . O ? ? A NA 177 A HOH 201 1_555 ? ? ? ? ? ? ? 2.497 ?
metalc13 metalc ? ? D NA . NA ? ? ? 1_555 I HOH . O ? ? A NA 178 A HOH 247 1_555 ? ? ? ? ? ? ? 2.855 ?
metalc14 metalc ? ? D NA . NA ? ? ? 1_555 I HOH . O ? ? A NA 178 A HOH 245 1_555 ? ? ? ? ? ? ? 2.655 ?
metalc15 metalc ? ? D NA . NA ? ? ? 1_555 I HOH . O ? ? A NA 178 A HOH 263 1_555 ? ? ? ? ? ? ? 2.500 ?
#
_struct_conn_type.id metalc
_struct_conn_type.criteria ?
_struct_conn_type.reference ?
#
_struct_mon_prot_cis.pdbx_id 1
_struct_mon_prot_cis.label_comp_id LEU
_struct_mon_prot_cis.label_seq_id 33
_struct_mon_prot_cis.label_asym_id A
_struct_mon_prot_cis.label_alt_id .
_struct_mon_prot_cis.pdbx_PDB_ins_code ?
_struct_mon_prot_cis.auth_comp_id LEU
_struct_mon_prot_cis.auth_seq_id 12
_struct_mon_prot_cis.auth_asym_id A
_struct_mon_prot_cis.pdbx_label_comp_id_2 PRO
_struct_mon_prot_cis.pdbx_label_seq_id_2 34
_struct_mon_prot_cis.pdbx_label_asym_id_2 A
_struct_mon_prot_cis.pdbx_PDB_ins_code_2 ?
_struct_mon_prot_cis.pdbx_auth_comp_id_2 PRO
_struct_mon_prot_cis.pdbx_auth_seq_id_2 13
_struct_mon_prot_cis.pdbx_auth_asym_id_2 A
_struct_mon_prot_cis.pdbx_PDB_model_num 1
_struct_mon_prot_cis.pdbx_omega_angle -0.44
#
loop_
_struct_sheet.id
_struct_sheet.type
_struct_sheet.number_strands
_struct_sheet.details
A ? 7 ?
B ? 2 ?
#
loop_
_struct_sheet_order.sheet_id
_struct_sheet_order.range_id_1
_struct_sheet_order.range_id_2
_struct_sheet_order.offset
_struct_sheet_order.sense
A 1 2 ? anti-parallel
A 2 3 ? anti-parallel
A 3 4 ? parallel
A 4 5 ? anti-parallel
A 5 6 ? anti-parallel
A 6 7 ? anti-parallel
B 1 2 ? anti-parallel
#
loop_
_struct_sheet_range.sheet_id
_struct_sheet_range.id
_struct_sheet_range.beg_label_comp_id
_struct_sheet_range.beg_label_asym_id
_struct_sheet_range.beg_label_seq_id
_struct_sheet_range.pdbx_beg_PDB_ins_code
_struct_sheet_range.end_label_comp_id
_struct_sheet_range.end_label_asym_id
_struct_sheet_range.end_label_seq_id
_struct_sheet_range.pdbx_end_PDB_ins_code
_struct_sheet_range.beg_auth_comp_id
_struct_sheet_range.beg_auth_asym_id
_struct_sheet_range.beg_auth_seq_id
_struct_sheet_range.end_auth_comp_id
_struct_sheet_range.end_auth_asym_id
_struct_sheet_range.end_auth_seq_id
A 1 VAL A 172 ? ASP A 178 ? VAL A 151 ASP A 157
A 2 VAL A 106 ? ASP A 119 ? VAL A 85 ASP A 98
A 3 GLY A 122 ? PRO A 131 ? GLY A 101 PRO A 110
A 4 VAL A 91 ? VAL A 95 ? VAL A 70 VAL A 74
A 5 ASN A 76 ? ILE A 80 ? ASN A 55 ILE A 59
A 6 PHE A 37 ? ILE A 43 ? PHE A 16 ILE A 22
A 7 VAL A 106 ? ASP A 119 ? VAL A 85 ASP A 98
B 1 VAL A 50 ? ASP A 55 ? VAL A 29 ASP A 34
B 2 LEU A 60 ? PHE A 66 ? LEU A 39 PHE A 45
#
loop_
_pdbx_struct_sheet_hbond.sheet_id
_pdbx_struct_sheet_hbond.range_id_1
_pdbx_struct_sheet_hbond.range_id_2
_pdbx_struct_sheet_hbond.range_1_label_atom_id
_pdbx_struct_sheet_hbond.range_1_label_comp_id
_pdbx_struct_sheet_hbond.range_1_label_asym_id
_pdbx_struct_sheet_hbond.range_1_label_seq_id
_pdbx_struct_sheet_hbond.range_1_PDB_ins_code
_pdbx_struct_sheet_hbond.range_1_auth_atom_id
_pdbx_struct_sheet_hbond.range_1_auth_comp_id
_pdbx_struct_sheet_hbond.range_1_auth_asym_id
_pdbx_struct_sheet_hbond.range_1_auth_seq_id
_pdbx_struct_sheet_hbond.range_2_label_atom_id
_pdbx_struct_sheet_hbond.range_2_label_comp_id
_pdbx_struct_sheet_hbond.range_2_label_asym_id
_pdbx_struct_sheet_hbond.range_2_label_seq_id
_pdbx_struct_sheet_hbond.range_2_PDB_ins_code
_pdbx_struct_sheet_hbond.range_2_auth_atom_id
_pdbx_struct_sheet_hbond.range_2_auth_comp_id
_pdbx_struct_sheet_hbond.range_2_auth_asym_id
_pdbx_struct_sheet_hbond.range_2_auth_seq_id
A 1 2 O GLY A 176 ? O GLY A 155 N LYS A 116 ? N LYS A 95
A 2 3 N LEU A 115 ? N LEU A 94 O LYS A 126 ? O LYS A 105
A 3 4 O ALA A 129 ? O ALA A 108 N LEU A 94 ? N LEU A 73
A 4 5 O VAL A 93 ? O VAL A 72 N GLY A 78 ? N GLY A 57
A 5 6 O PHE A 79 ? O PHE A 58 N ILE A 40 ? N ILE A 19
A 6 7 N PHE A 37 ? N PHE A 16 O ALA A 109 ? O ALA A 88
B 1 2 N ASP A 55 ? N ASP A 34 O LEU A 60 ? O LEU A 39
#
loop_
_struct_site.id
_struct_site.pdbx_evidence_code
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
_struct_site.pdbx_auth_ins_code
_struct_site.pdbx_num_residues
_struct_site.details
AC1 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE K A 176'
AC2 Software ? ? ? ? 6 'BINDING SITE FOR RESIDUE NA A 177'
AC3 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE NA A 178'
AC4 Software ? ? ? ? 14 'BINDING SITE FOR RESIDUE POP A 179'
AC5 Software ? ? ? ? 7 'BINDING SITE FOR RESIDUE PG4 A 180'
AC6 Software ? ? ? ? 4 'BINDING SITE FOR RESIDUE PEG A 181'
AC7 Software ? ? ? ? 3 'BINDING SITE FOR RESIDUE PEG A 182'
#
loop_
_struct_site_gen.id
_struct_site_gen.site_id
_struct_site_gen.pdbx_num_res
_struct_site_gen.label_comp_id
_struct_site_gen.label_asym_id
_struct_site_gen.label_seq_id
_struct_site_gen.pdbx_auth_ins_code
_struct_site_gen.auth_comp_id
_struct_site_gen.auth_asym_id
_struct_site_gen.auth_seq_id
_struct_site_gen.label_atom_id
_struct_site_gen.label_alt_id
_struct_site_gen.symmetry
_struct_site_gen.details
1 AC1 3 ASP A 32 ? ASP A 11 . ? 1_555 ?
2 AC1 3 LEU A 33 ? LEU A 12 . ? 1_555 ?
3 AC1 3 GLN A 35 ? GLN A 14 . ? 1_555 ?
4 AC2 6 ASP A 119 ? ASP A 98 . ? 1_555 ?
5 AC2 6 ASP A 124 ? ASP A 103 . ? 1_555 ?
6 AC2 6 LYS A 164 ? LYS A 143 . ? 1_555 ?
7 AC2 6 POP E . ? POP A 179 . ? 1_555 ?
8 AC2 6 HOH I . ? HOH A 201 . ? 1_555 ?
9 AC2 6 HOH I . ? HOH A 257 . ? 1_555 ?
10 AC3 7 ASP A 87 ? ASP A 66 . ? 1_555 ?
11 AC3 7 ASP A 92 ? ASP A 71 . ? 1_555 ?
12 AC3 7 ASP A 124 ? ASP A 103 . ? 1_555 ?
13 AC3 7 ALA A 125 ? ALA A 104 . ? 1_555 ?
14 AC3 7 HOH I . ? HOH A 245 . ? 1_555 ?
15 AC3 7 HOH I . ? HOH A 247 . ? 1_555 ?
16 AC3 7 HOH I . ? HOH A 263 . ? 1_555 ?
17 AC4 14 LYS A 51 ? LYS A 30 . ? 1_555 ?
18 AC4 14 ARG A 65 ? ARG A 44 . ? 1_555 ?
19 AC4 14 TYR A 77 ? TYR A 56 . ? 1_555 ?
20 AC4 14 ASP A 124 ? ASP A 103 . ? 1_555 ?
21 AC4 14 LYS A 126 ? LYS A 105 . ? 1_555 ?
22 AC4 14 TYR A 163 ? TYR A 142 . ? 1_555 ?
23 AC4 14 LYS A 164 ? LYS A 143 . ? 1_555 ?
24 AC4 14 NA C . ? NA A 177 . ? 1_555 ?
25 AC4 14 HOH I . ? HOH A 200 . ? 1_555 ?
26 AC4 14 HOH I . ? HOH A 221 . ? 1_555 ?
27 AC4 14 HOH I . ? HOH A 238 . ? 1_555 ?
28 AC4 14 HOH I . ? HOH A 239 . ? 1_555 ?
29 AC4 14 HOH I . ? HOH A 260 . ? 1_555 ?
30 AC4 14 HOH I . ? HOH A 267 . ? 1_555 ?
31 AC5 7 GLY A 30 ? GLY A 9 . ? 7_555 ?
32 AC5 7 LYS A 31 ? LYS A 10 . ? 7_555 ?
33 AC5 7 ASP A 32 ? ASP A 11 . ? 7_555 ?
34 AC5 7 LEU A 33 ? LEU A 12 . ? 7_555 ?
35 AC5 7 GLN A 35 ? GLN A 14 . ? 1_555 ?