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1JGM

High Resolution Structure of the Cadmium-containing Phosphotriesterase from Pseudomonas diminuta

Replaces:  1I03
Functional Information from GO Data
ChainGOidnamespacecontents
A0004063molecular_functionaryldialkylphosphatase activity
A0005886cellular_componentplasma membrane
A0008270molecular_functionzinc ion binding
A0009056biological_processcatabolic process
A0016020cellular_componentmembrane
A0016787molecular_functionhydrolase activity
A0016788molecular_functionhydrolase activity, acting on ester bonds
A0046872molecular_functionmetal ion binding
B0004063molecular_functionaryldialkylphosphatase activity
B0005886cellular_componentplasma membrane
B0008270molecular_functionzinc ion binding
B0009056biological_processcatabolic process
B0016020cellular_componentmembrane
B0016787molecular_functionhydrolase activity
B0016788molecular_functionhydrolase activity, acting on ester bonds
B0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CD A 1
ChainResidue
AEDO8
AHIS55
AHIS57
AKCX169
AASP301
AHOH590

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CD A 2
ChainResidue
AHOH590
AHOH646
AHOH699
AKCX169
AHIS201
AHIS230

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CD B 3
ChainResidue
BEDO7
BHIS55
BHIS57
BKCX169
BASP301
BHOH721

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CD B 4
ChainResidue
BKCX169
BHIS201
BHIS230
BHOH606
BHOH681
BHOH721

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA A 5
ChainResidue
AASN38
AILE154
AHOH371
AHOH376
AHOH557
AHOH615

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NA B 6
ChainResidue
BASN38
BILE154
BHOH391
BHOH559
BHOH566
BHOH593

site_idAC7
Number of Residues10
DetailsBINDING SITE FOR RESIDUE EDO B 7
ChainResidue
BCD3
BEDO20
BHIS57
BTRP131
BKCX169
BPHE306
BSER308
BEDO368
BHOH606
BHOH721

site_idAC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO A 8
ChainResidue
ACD1
AEDO22
AHIS57
ATRP131
AKCX169
APHE306
AHOH648
AHOH699

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 9
ChainResidue
AARG91
BARG189
BHOH481
BHOH567
BHOH700

site_idBC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 10
ChainResidue
AHOH469
AHOH568
AHOH577
AHOH602

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 11
ChainResidue
AVAL84
AGLU115
AALA119
AHOH430
AHOH595

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 12
ChainResidue
AEDO13
ATHR147
AARG189
AHOH487
AHOH554
AHOH607
BARG91

site_idBC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 13
ChainResidue
AEDO12
AHOH607
BARG91
BASP121

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 14
ChainResidue
BEDO24
BARG76
BLYS77
BGLU115
BHOH424
BHOH610

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 15
ChainResidue
BGLY305
BPHE306
BMET314
BHOH540
BHOH723

site_idBC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO B 16
ChainResidue
BPRO256
BVAL320
BPHE327
BHOH575

site_idBC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO B 17
ChainResidue
BPRO135
BHOH370
BHOH372
AASP133
APRO135
AHOH712
BASP133
BPRO134

site_idBC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE EDO A 18
ChainResidue
AHOH390

site_idCC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 19
ChainResidue
APRO256
ATRP277
AVAL320
APHE327
AHOH591

site_idCC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 20
ChainResidue
BEDO7
BHIS257
BASP301
BHOH721
BHOH742

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 21
ChainResidue
AARG41
APRO43
BGLU338
BHOH580

site_idCC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 22
ChainResidue
AEDO8
APHE306
ASER308
AHOH597

site_idCC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 23
ChainResidue
ASER224
AARG225
ALEU249
AARG356
APHE357
AHOH609

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 24
ChainResidue
BEDO14
BALA80
BGLU81
BGLU115
BHOH648

site_idCC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO A 25
ChainResidue
AALA266
ASER269
AALA270

site_idCC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 26
ChainResidue
AHOH586
AHOH671
BTYR156
BHOH466
BHOH656

site_idCC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 27
ChainResidue
APHE73
AGLY74
AALA78
AHOH589
AHOH629

site_idDC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO A 28
ChainResidue
ALYS285
AILE288
AASP289
AVAL341
APRO342
AHOH523

site_idDC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 29
ChainResidue
AGLY305
APHE306
AMET314
AHOH422
AHOH526

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO B 366
ChainResidue
AARG152
ATYR156
BGLU71
BHOH377
BHOH658

site_idDC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 367
ChainResidue
AILE333
AARG337
AGLN343
AHOH394
BTYR156
BHOH469
BHOH674

site_idDC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE EDO A 366
ChainResidue
ATHR173
AHOH605

site_idDC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 368
ChainResidue
BEDO7
BSER308
BTYR309

site_idDC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PEL B 369
ChainResidue
BLYS77
BMET293
BGLY348
BASN353

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PEL A 367
ChainResidue
ALYS77
AMET293
ATHR345
AGLY348
AILE349
AASN353

site_idDC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PEL A 368
ChainResidue
AARG88
AARG89
AHOH580
BLEU362
BARG363

Functional Information from PROSITE/UniProt
site_idPS01322
Number of Residues9
DetailsPHOSPHOTRIESTERASE_1 Phosphotriesterase family signature 1. GfTLtHEHI
ChainResidueDetails
AGLY50-ILE58

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues10
DetailsBINDING: BINDING => ECO:0000269|PubMed:7794910, ECO:0007744|PDB:1DPM, ECO:0007744|PDB:1EYW, ECO:0007744|PDB:1EZ2, ECO:0007744|PDB:1HZY, ECO:0007744|PDB:2O4M, ECO:0007744|PDB:2O4Q, ECO:0007744|PDB:2OB3, ECO:0007744|PDB:2OQL
ChainResidueDetails
AHIS55
BASP301
AHIS57
AHIS201
AHIS230
AASP301
BHIS55
BHIS57
BHIS201
BHIS230

site_idSWS_FT_FI2
Number of Residues2
DetailsBINDING: via carbamate group => ECO:0000269|PubMed:7794910, ECO:0007744|PDB:1DPM, ECO:0007744|PDB:1EYW, ECO:0007744|PDB:1EZ2, ECO:0007744|PDB:1HZY, ECO:0007744|PDB:2O4M, ECO:0007744|PDB:2O4Q, ECO:0007744|PDB:2OB3, ECO:0007744|PDB:2OQL
ChainResidueDetails
AKCX169
BKCX169

site_idSWS_FT_FI3
Number of Residues2
DetailsMOD_RES: N6-carboxylysine => ECO:0000255|PROSITE-ProRule:PRU00679, ECO:0000269|PubMed:7794910, ECO:0007744|PDB:1DPM, ECO:0007744|PDB:1EYW, ECO:0007744|PDB:1EZ2, ECO:0007744|PDB:1HZY, ECO:0007744|PDB:2O4M, ECO:0007744|PDB:2O4Q, ECO:0007744|PDB:2OB3, ECO:0007744|PDB:2OQL
ChainResidueDetails
AKCX169
BKCX169

Catalytic Information from CSA
site_idMCSA1
Number of Residues8
DetailsM-CSA 159
ChainResidueDetails
AHIS55metal ligand
AHIS57metal ligand
AKCX169metal ligand
AHIS201metal ligand
AHIS230metal ligand
AASP233hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
AHIS254hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
AASP301hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor

site_idMCSA2
Number of Residues8
DetailsM-CSA 159
ChainResidueDetails
BHIS55metal ligand
BHIS57metal ligand
BKCX169metal ligand
BHIS201metal ligand
BHIS230metal ligand
BASP233hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
BHIS254hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
BASP301hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor

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PDB entries from 2024-04-24

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