Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4AC7

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

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	0005737	cellular_component	cytoplasm
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
C	0043419	biological_process	urea catabolic process
C	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO A 1101

Chain	Residue
A	GLY50
C	LYS559
A	LYS51
A	THR52
A	PHE86
A	ASP88
A	HOH2092
A	HOH2093
C	VAL309
C	ASN310

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1102

Chain	Residue
A	LYS29
A	ASP67
A	ASP68
A	HOH2033
A	HOH2038

site_id	AC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 1103

Chain	Residue
A	ASN4
A	ALA6
A	LYS10
A	HOH2005
A	HOH2084
C	PHE568
C	PHE570
C	HOH2294

site_id	AC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 1127

Chain	Residue
B	ASP101
B	HOH2141
C	PRO229
C	HOH2214

site_id	AC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE SO4 B 1128

Chain	Residue
B	ARG116

site_id	AC6
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	OH1571
C	FLC1572

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE NI C 601

Chain	Residue
C	HIS137
C	HIS139
C	KCX220
C	ASP363
C	NI600
C	OH1571
C	FLC1572

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE OH C 1571

Chain	Residue
C	HIS137
C	KCX220
C	HIS275
C	ASP363
C	NI600
C	NI601
C	FLC1572

site_id	AC9
Number of Residues	18
Details	BINDING SITE FOR RESIDUE FLC C 1572

Chain	Residue
C	HIS139
C	LYS169
C	ALA170
C	KCX220
C	HIS222
C	ASP224
C	HIS249
C	GLY280
C	ARG339
C	ASP363
C	ALA366
C	MET367
C	NI600
C	NI601
C	OH1571
C	HOH2170
C	HOH2209
C	HOH2274

site_id	BC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1573

Chain	Residue
C	ASP34
C	THR36
C	TYR38
C	HOH2035
C	HOH2050
C	HOH2433

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO C 1574

Chain	Residue
C	ASP286
C	ALA289
C	ILE537
C	ILE539
C	HOH2234

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1575

Chain	Residue
B	GLN41
B	HOH2068
C	GLY46
C	LEU325
C	HOH2276
C	HOH2434

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1576

Chain	Residue
C	TYR93
C	GLU423
C	GLN501
C	ARG513
C	ILE514
C	HOH2435

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO C 1577

Chain	Residue
C	TYR35
C	TYR83
C	ILE97
C	GLU429
C	HOH2032
C	HOH2436

site_id	BC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO C 1578

Chain	Residue
C	GLU181
C	ARG62
C	PRO177

site_id	BC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 C 1579

Chain	Residue
C	SER204
C	ILE205
C	HOH2084
C	HOH2189
C	HOH2194

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 C 1580

Chain	Residue
C	VAL558
C	LYS559
C	GLU560
C	HOH2422

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE SO4 C 1581

Chain	Residue
C	LYS511
C	LYS511
C	LYS511

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)