Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6I9Y

The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urease in complex with Au(I) ions

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	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	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

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue EDO A 201

Chain	Residue
A	GLY50
A	LYS51
A	THR52
A	PRO87
C	VAL309
C	ASN310
C	LYS559

site_id	AC2
Number of Residues	6
Details	binding site for residue SO4 A 202

Chain	Residue
A	GLU58
C	PRO330
C	VAL333
C	ALA334
A	ALA54
A	MET57

site_id	AC3
Number of Residues	7
Details	binding site for residue SO4 A 203

Chain	Residue
A	ALA6
A	GLU7
A	LYS10
A	THR85
A	THR90
C	PHE568
C	PHE570

site_id	AC4
Number of Residues	4
Details	binding site for residue EDO B 201

Chain	Residue
B	ASP101
B	HOH323
C	PRO229
C	EDO617

site_id	AC5
Number of Residues	5
Details	binding site for residue EDO B 202

Chain	Residue
A	PHE42
A	GLU59
A	HIS62
B	GLU84
B	HOH324

site_id	AC6
Number of Residues	3
Details	binding site for residue SO4 B 203

Chain	Residue
B	ILE30
B	ARG31
B	HOH317

site_id	AC7
Number of Residues	2
Details	binding site for residue SO4 B 204

Chain	Residue
B	ARG116
B	HOH307

site_id	AC8
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	OH603
C	HOH713

site_id	AC9
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	OH603
C	HOH771

site_id	AD1
Number of Residues	9
Details	binding site for residue OH C 603

Chain	Residue
C	HIS137
C	KCX220
C	HIS275
C	ASP363
C	NI601
C	NI602
C	HOH713
C	HOH771
C	HOH820

site_id	AD2
Number of Residues	3
Details	binding site for residue EDO C 604

Chain	Residue
C	SER204
C	ILE205
C	ALA206

site_id	AD3
Number of Residues	5
Details	binding site for residue EDO C 605

Chain	Residue
C	ASP286
C	ILE537
C	ASP538
C	ILE539
C	HOH707

site_id	AD4
Number of Residues	3
Details	binding site for residue EDO C 606

Chain	Residue
C	HIS293
C	ASN295
C	HOH755

site_id	AD5
Number of Residues	3
Details	binding site for residue EDO C 607

Chain	Residue
C	PRO342
C	ALA346
C	CYS555

site_id	AD6
Number of Residues	2
Details	binding site for residue EDO C 608

Chain	Residue
B	SER71
C	LYS48

site_id	AD7
Number of Residues	4
Details	binding site for residue EDO C 609

Chain	Residue
C	ASP34
C	THR36
C	TYR38
C	HOH863

site_id	AD8
Number of Residues	5
Details	binding site for residue SO4 C 610

Chain	Residue
C	TYR35
C	ILE97
C	GLU429
C	HOH710
C	HOH884

site_id	AD9
Number of Residues	3
Details	binding site for residue SO4 C 611

Chain	Residue
C	ILE500
C	ARG513
C	ILE514

site_id	AE1
Number of Residues	4
Details	binding site for residue AU C 612

Chain	Residue
C	CYS322
C	HIS323
C	AU613
C	SO4615

site_id	AE2
Number of Residues	4
Details	binding site for residue AU C 613

Chain	Residue
C	CYS322
C	MET367
C	AU612
C	SO4615

site_id	AE3
Number of Residues	2
Details	binding site for residue AU C 614

Chain	Residue
C	GLN387
C	CYS555

site_id	AE4
Number of Residues	11
Details	binding site for residue SO4 C 615

Chain	Residue
C	HIS323
C	ARG339
C	AU612
C	AU613
C	EDO616
C	HOH713
C	HOH761
C	HOH820
C	GLU223
C	ASP224
C	HIS249

site_id	AE5
Number of Residues	5
Details	binding site for residue EDO C 616

Chain	Residue
C	GLY46
C	LYS48
C	ASP224
C	HIS323
C	SO4615

site_id	AE6
Number of Residues	6
Details	binding site for residue EDO C 617

Chain	Residue
B	EDO201
C	ASP233
C	ARG264
C	ALA265
C	ASN267
C	ARG269

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)