Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6QDY

The crystal structure of Sporosarcina pasteurii urease in complex with its substrate urea

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 201

Chain	Residue
A	GLY50
C	HOH1080
A	LYS51
A	THR52
A	PHE86
A	PRO87
A	ASP88
C	VAL309
C	ASN310
C	LYS559

site_id	AC2
Number of Residues	8
Details	binding site for residue EDO A 202

Chain	Residue
A	ASN4
A	ALA6
A	LYS10
A	HOH305
A	HOH314
C	PHE568
C	PHE570
C	HOH993

site_id	AC3
Number of Residues	6
Details	binding site for residue EDO A 203

Chain	Residue
A	CXM1
A	TYR32
A	ASP79
A	HOH324
C	HOH1003
C	HOH1026

site_id	AC4
Number of Residues	7
Details	binding site for residue EDO B 201

Chain	Residue
B	ASP101
B	HOH309
B	HOH319
C	PRO229
C	ASP233
C	ALA265
C	HOH1100

site_id	AC5
Number of Residues	7
Details	binding site for residue EDO B 202

Chain	Residue
A	PHE42
A	GLU59
A	HIS62
A	HOH376
A	HOH408
B	GLU84
B	HOH411

site_id	AC6
Number of Residues	2
Details	binding site for residue SO4 B 203

Chain	Residue
B	ARG116
B	HOH417

site_id	AC7
Number of Residues	8
Details	binding site for residue NI C 601

Chain	Residue
C	KCX220
C	HIS222
C	HIS249
C	HIS275
C	GLY280
C	NI602
C	F610
C	URE611

site_id	AC8
Number of Residues	7
Details	binding site for residue NI C 602

Chain	Residue
C	HIS137
C	HIS139
C	KCX220
C	ASP363
C	NI601
C	F610
C	URE611

site_id	AC9
Number of Residues	6
Details	binding site for residue EDO C 603

Chain	Residue
C	ASP34
C	THR36
C	TYR38
C	HOH756
C	HOH803
C	HOH846

site_id	AD1
Number of Residues	8
Details	binding site for residue EDO C 604

Chain	Residue
C	TYR35
C	TYR83
C	ILE97
C	GLU429
C	HOH704
C	HOH804
C	HOH1029
C	HOH1040

site_id	AD2
Number of Residues	7
Details	binding site for residue EDO C 605

Chain	Residue
C	ASP286
C	ALA289
C	ILE537
C	ILE539
C	HOH845
C	HOH975
C	HOH1049

site_id	AD3
Number of Residues	7
Details	binding site for residue EDO C 606

Chain	Residue
B	PRO70
B	THR73
C	GLN7
C	SER11
C	HOH732
C	HOH827
C	HOH925

site_id	AD4
Number of Residues	7
Details	binding site for residue EDO C 607

Chain	Residue
B	PRO39
B	ARG76
B	GLU78
B	HOH450
C	ASP337
C	SER338
C	TYR544

site_id	AD5
Number of Residues	6
Details	binding site for residue EDO C 608

Chain	Residue
C	VAL558
C	LYS559
C	GLU560
C	HOH1007
C	HOH1010
C	HOH1074

site_id	AD6
Number of Residues	9
Details	binding site for residue SO4 C 609

Chain	Residue
C	TYR12
C	ASN43
C	LYS48
C	LYS326
C	ILE329
C	HOH1021
B	SER71
B	GLY72
C	SER11

site_id	AD7
Number of Residues	7
Details	binding site for residue F C 610

Chain	Residue
C	HIS137
C	KCX220
C	HIS275
C	ASP363
C	NI601
C	NI602
C	URE611

site_id	AD8
Number of Residues	13
Details	binding site for residue URE C 611

Chain	Residue
C	HIS139
C	ALA170
C	KCX220
C	HIS222
C	HIS249
C	GLY280
C	HIS323
C	ASP363
C	ALA366
C	MET367
C	NI601
C	NI602
C	F610

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)