Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1JGM

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

Replaces: 1I03

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0004063	molecular_function	aryldialkylphosphatase activity
A	0005886	cellular_component	plasma membrane
A	0008270	molecular_function	zinc ion binding
A	0009056	biological_process	catabolic process
A	0016787	molecular_function	hydrolase activity
A	0016788	molecular_function	hydrolase activity, acting on ester bonds
A	0046872	molecular_function	metal ion binding
B	0004063	molecular_function	aryldialkylphosphatase activity
B	0005886	cellular_component	plasma membrane
B	0008270	molecular_function	zinc ion binding
B	0009056	biological_process	catabolic process
B	0016787	molecular_function	hydrolase activity
B	0016788	molecular_function	hydrolase activity, acting on ester bonds
B	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CD A 1

Chain	Residue
A	EDO8
A	HIS55
A	HIS57
A	KCX169
A	ASP301
A	HOH590

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CD A 2

Chain	Residue
A	HOH590
A	HOH646
A	HOH699
A	KCX169
A	HIS201
A	HIS230

site_id	AC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CD B 3

Chain	Residue
B	EDO7
B	HIS55
B	HIS57
B	KCX169
B	ASP301
B	HOH721

site_id	AC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE CD B 4

Chain	Residue
B	KCX169
B	HIS201
B	HIS230
B	HOH606
B	HOH681
B	HOH721

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA A 5

Chain	Residue
A	ASN38
A	ILE154
A	HOH371
A	HOH376
A	HOH557
A	HOH615

site_id	AC6
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NA B 6

Chain	Residue
B	ASN38
B	ILE154
B	HOH391
B	HOH559
B	HOH566
B	HOH593

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO B 7

Chain	Residue
B	CD3
B	EDO20
B	HIS57
B	TRP131
B	KCX169
B	PHE306
B	SER308
B	EDO368
B	HOH606
B	HOH721

site_id	AC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 8

Chain	Residue
A	CD1
A	EDO22
A	HIS57
A	TRP131
A	KCX169
A	PHE306
A	HOH648
A	HOH699

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 9

Chain	Residue
A	ARG91
B	ARG189
B	HOH481
B	HOH567
B	HOH700

site_id	BC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 10

Chain	Residue
A	HOH469
A	HOH568
A	HOH577
A	HOH602

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 11

Chain	Residue
A	VAL84
A	GLU115
A	ALA119
A	HOH430
A	HOH595

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 12

Chain	Residue
A	EDO13
A	THR147
A	ARG189
A	HOH487
A	HOH554
A	HOH607
B	ARG91

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 13

Chain	Residue
A	EDO12
A	HOH607
B	ARG91
B	ASP121

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 14

Chain	Residue
B	EDO24
B	ARG76
B	LYS77
B	GLU115
B	HOH424
B	HOH610

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 15

Chain	Residue
B	GLY305
B	PHE306
B	MET314
B	HOH540
B	HOH723

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 16

Chain	Residue
B	PRO256
B	VAL320
B	PHE327
B	HOH575

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO B 17

Chain	Residue
B	PRO135
B	HOH370
B	HOH372
A	ASP133
A	PRO135
A	HOH712
B	ASP133
B	PRO134

site_id	BC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE EDO A 18

Chain	Residue
A	HOH390

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 19

Chain	Residue
A	PRO256
A	TRP277
A	VAL320
A	PHE327
A	HOH591

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 20

Chain	Residue
B	EDO7
B	HIS257
B	ASP301
B	HOH721
B	HOH742

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 21

Chain	Residue
A	ARG41
A	PRO43
B	GLU338
B	HOH580

site_id	CC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 22

Chain	Residue
A	EDO8
A	PHE306
A	SER308
A	HOH597

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 23

Chain	Residue
A	SER224
A	ARG225
A	LEU249
A	ARG356
A	PHE357
A	HOH609

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 24

Chain	Residue
B	EDO14
B	ALA80
B	GLU81
B	GLU115
B	HOH648

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 25

Chain	Residue
A	ALA266
A	SER269
A	ALA270

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 26

Chain	Residue
A	HOH586
A	HOH671
B	TYR156
B	HOH466
B	HOH656

site_id	CC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 27

Chain	Residue
A	PHE73
A	GLY74
A	ALA78
A	HOH589
A	HOH629

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 28

Chain	Residue
A	LYS285
A	ILE288
A	ASP289
A	VAL341
A	PRO342
A	HOH523

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 29

Chain	Residue
A	GLY305
A	PHE306
A	MET314
A	HOH422
A	HOH526

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 366

Chain	Residue
A	ARG152
A	TYR156
B	GLU71
B	HOH377
B	HOH658

site_id	DC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 367

Chain	Residue
A	ILE333
A	ARG337
A	GLN343
A	HOH394
B	TYR156
B	HOH469
B	HOH674

site_id	DC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 366

Chain	Residue
A	THR173
A	HOH605

site_id	DC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 368

Chain	Residue
B	EDO7
B	SER308
B	TYR309

site_id	DC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PEL B 369

Chain	Residue
B	LYS77
B	MET293
B	GLY348
B	ASN353

site_id	DC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PEL A 367

Chain	Residue
A	LYS77
A	MET293
A	THR345
A	GLY348
A	ILE349
A	ASN353

site_id	DC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEL A 368

Chain	Residue
A	ARG88
A	ARG89
A	HOH580
B	LEU362
B	ARG363

Functional Information from PROSITE/UniProt

site_id	PS01322
Number of Residues	9
Details	PHOSPHOTRIESTERASE_1 Phosphotriesterase family signature 1. GfTLtHEHI

Chain	Residue	Details
A	GLY50-ILE58

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	10
Details	Binding site: {"evidences":[{"source":"PubMed","id":"7794910","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DPM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EYW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EZ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HZY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OB3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OQL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	2
Details	Binding site: {"description":"via carbamate group","evidences":[{"source":"PubMed","id":"7794910","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DPM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EYW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EZ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HZY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OB3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OQL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	2
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"PROSITE-ProRule","id":"PRU00679","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"7794910","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1DPM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EYW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1EZ2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1HZY","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2O4Q","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OB3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2OQL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	3
Details	Annotated By Reference To The Literature 1ez2

Chain	Residue	Details
A	HIS254
A	ASP233
A	ASP301

site_id	CSA2
Number of Residues	3
Details	Annotated By Reference To The Literature 1ez2

Chain	Residue	Details
B	HIS254
B	ASP233
B	ASP301

site_id	MCSA1
Number of Residues	8
Details	M-CSA 159

Chain	Residue	Details
A	HIS55	metal ligand
A	HIS57	metal ligand
A	KCX169	metal ligand
A	SER205	metal ligand
A	THR234	metal ligand
A	LEU237	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	SER258	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
A	GLY305	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor

site_id	MCSA2
Number of Residues	8
Details	M-CSA 159

Chain	Residue	Details
B	HIS55	metal ligand
B	HIS57	metal ligand
B	KCX169	metal ligand
B	SER205	metal ligand
B	THR234	metal ligand
B	LEU237	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	SER258	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
B	GLY305	hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)