Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5G4H

1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005737	cellular_component	cytoplasm
A	0009039	molecular_function	urease activity
A	0016151	molecular_function	nickel cation binding
A	0016787	molecular_function	hydrolase activity
A	0019627	biological_process	urea metabolic process
A	0043419	biological_process	urea catabolic process
B	0005737	cellular_component	cytoplasm
B	0009039	molecular_function	urease activity
B	0016787	molecular_function	hydrolase activity
B	0035550	cellular_component	urease complex
B	0043419	biological_process	urea catabolic process
C	0009039	molecular_function	urease activity
C	0016151	molecular_function	nickel cation binding
C	0016787	molecular_function	hydrolase activity
C	0016810	molecular_function	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE NI C 600

Chain	Residue
C	KCX220
C	HIS222
C	HIS249
C	HIS275
C	GLY280
C	NI601
C	OH1573
C	HOH2176

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NI C 601

Chain	Residue
C	HIS139
C	KCX220
C	ASP363
C	NI600
C	OH1573
C	HOH2153
C	HIS137

site_id	AC3
Number of Residues	12
Details	BINDING SITE FOR RESIDUE SO4 C 1572

Chain	Residue
C	HIS222
C	GLU223
C	ASP224
C	HIS249
C	GLY280
C	HIS323
C	ARG339
C	HOH2176
C	HOH2206
C	HOH2208
C	HOH2248
C	HOH2288

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OH C 1573

Chain	Residue
C	HIS137
C	KCX220
C	HIS275
C	ASP363
C	NI600
C	NI601
C	HOH2153
C	HOH2176
C	HOH2248

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 1574

Chain	Residue
C	VAL558
C	LYS559
C	GLU560
C	HOH2415

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 1101

Chain	Residue
A	MET70
A	GLU71
A	HOH2095
C	ARG566

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 B 1127

Chain	Residue
B	ARG116

site_id	AC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO C 1575

Chain	Residue
A	GLY50
A	LYS51
A	THR52
A	PHE86
A	ASP88
C	VAL309
C	ASN310
C	LYS559
C	HOH2425

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1576

Chain	Residue
C	ASP34
C	THR36
C	TYR38
C	HOH2048
C	HOH2060
C	HOH2426

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1577

Chain	Residue
C	ASP286
C	ALA289
C	ILE537
C	ILE539
C	HOH2232
C	HOH2404

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 1102

Chain	Residue
A	GLY27
A	LEU28
A	LYS29
A	ASP67
A	ASP68
A	HOH2032
A	HOH2040

site_id	BC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 1578

Chain	Residue
B	HOH2079
C	GLY46
C	HIS323
C	LEU325
C	PHE335
C	HOH2067
C	HOH2203

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO C 1579

Chain	Residue
B	SER71
C	TYR12
C	LYS48
C	HOH2019

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1580

Chain	Residue
C	TYR35
C	TYR83
C	ILE97
C	GLU429
C	HOH2045
C	HOH2428

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO C 1581

Chain	Residue
A	ASN4
A	LYS10
A	HOH2088
C	PHE568
C	PHE570
C	HOH2291
C	HOH2429

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 1128

Chain	Residue
C	PRO229
C	ASP233
C	HOH2213
C	HOH2240
B	ASP101
B	HOH2127

site_id	BC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 1582

Chain	Residue
C	THR237
C	ASP240
C	ARG269

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1583

Chain	Residue
C	HIS422
C	GLU423
C	GLY430
C	GLN501
C	HOH2327
C	HOH2383

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1584

Chain	Residue
C	TYR93
C	GLU423
C	GLN501
C	ARG513
C	ILE514
C	HOH2431

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1103

Chain	Residue
A	CXM1
A	TYR32
A	ASP79
A	HOH2085
A	HOH2096

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1585

Chain	Residue
C	PRO143
C	GLY189
C	PRO191
C	ARG478
C	HOH2071
C	HOH2158

site_id	CC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 1586

Chain	Residue
C	PRO177
C	TRP178
C	GLU181

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 B 1129

Chain	Residue
B	ILE30
B	ARG31
B	HOH2058

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 1587

Chain	Residue
C	SER204
C	ILE205
C	HOH2190
C	HOH2194

site_id	CC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OH C 1573

Chain	Residue
C	HIS137
C	KCX220
C	HIS275
C	ASP363
C	NI600
C	NI601
C	HOH2153
C	HOH2176
C	HOH2248

site_id	CC8
Number of Residues	12
Details	Binding site for Di-peptide CYS C 322 and CAQ C1571

Chain	Residue
C	MET318
C	LEU319
C	MET320
C	VAL321
C	HIS323
C	HIS324
C	ILE468
C	PRO469
C	THR470
C	HOH2172
C	HOH2173
C	HOH2424

Functional Information from PROSITE/UniProt

site_id	PS00145
Number of Residues	17
Details	UREASE_2 Urease active site. MVCHHLkqnIpeDVaFA

Chain	Residue	Details
C	MET320-ALA336

site_id	PS01120
Number of Residues	14
Details	UREASE_1 Urease nickel ligands signature. TAGGIDtHVHfinP

Chain	Residue	Details
C	THR130-PRO143

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	1
Details	Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_01953","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368287","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10766443","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11713685","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15038715","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30969470","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"1998","firstPage":"268","lastPage":"273","volume":"3","journal":"J. Biol. Inorg. Chem.","title":"The complex of Bacillus pasteurii urease with beta-mercaptoethanol from X-ray data at 1.65-A resolution.","authors":["Benini S.","Rypniewski W.R.","Wilson K.S.","Ciurli S.","Mangani S."],"citationCrossReferences":[{"database":"DOI","id":"10.1007/s007750050231"}]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	5
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30969470","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	1
Details	Binding site: {"description":"via carbamate group","evidences":[{"source":"HAMAP-Rule","id":"MF_01953","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368287","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10766443","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11713685","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15038715","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30969470","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"1998","firstPage":"268","lastPage":"273","volume":"3","journal":"J. Biol. Inorg. Chem.","title":"The complex of Bacillus pasteurii urease with beta-mercaptoethanol from X-ray data at 1.65-A resolution.","authors":["Benini S.","Rypniewski W.R.","Wilson K.S.","Ciurli S.","Mangani S."],"citationCrossReferences":[{"database":"DOI","id":"10.1007/s007750050231"}]}}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	1
Details	Modified residue: {"description":"N6-carboxylysine","evidences":[{"source":"HAMAP-Rule","id":"MF_01953","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10368287","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10766443","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11713685","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15038715","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30969470","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"journal article","publicationDate":"1998","firstPage":"268","lastPage":"273","volume":"3","journal":"J. Biol. Inorg. Chem.","title":"The complex of Bacillus pasteurii urease with beta-mercaptoethanol from X-ray data at 1.65-A resolution.","authors":["Benini S.","Rypniewski W.R.","Wilson K.S.","Ciurli S.","Mangani S."],"citationCrossReferences":[{"database":"DOI","id":"10.1007/s007750050231"}]}},{"source":"PDB","id":"1IE7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S3T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1UBP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2UBP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4UBP","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)