Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3B9X

Crystal structure of the E. coli pyrimidine nucleoside hydrolase YeiK in complex with inosine

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005509	molecular_function	calcium ion binding
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006152	biological_process	purine nucleoside catabolic process
A	0006206	biological_process	pyrimidine nucleobase metabolic process
A	0008477	molecular_function	purine nucleosidase activity
A	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
A	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
A	0032991	cellular_component	protein-containing complex
A	0042802	molecular_function	identical protein binding
A	0045437	molecular_function	uridine nucleosidase activity
A	0046133	biological_process	pyrimidine ribonucleoside catabolic process
A	0046872	molecular_function	metal ion binding
A	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
A	0051289	biological_process	protein homotetramerization
B	0005509	molecular_function	calcium ion binding
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006152	biological_process	purine nucleoside catabolic process
B	0006206	biological_process	pyrimidine nucleobase metabolic process
B	0008477	molecular_function	purine nucleosidase activity
B	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
B	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
B	0032991	cellular_component	protein-containing complex
B	0042802	molecular_function	identical protein binding
B	0045437	molecular_function	uridine nucleosidase activity
B	0046133	biological_process	pyrimidine ribonucleoside catabolic process
B	0046872	molecular_function	metal ion binding
B	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
B	0051289	biological_process	protein homotetramerization
C	0005509	molecular_function	calcium ion binding
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006152	biological_process	purine nucleoside catabolic process
C	0006206	biological_process	pyrimidine nucleobase metabolic process
C	0008477	molecular_function	purine nucleosidase activity
C	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
C	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
C	0032991	cellular_component	protein-containing complex
C	0042802	molecular_function	identical protein binding
C	0045437	molecular_function	uridine nucleosidase activity
C	0046133	biological_process	pyrimidine ribonucleoside catabolic process
C	0046872	molecular_function	metal ion binding
C	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
C	0051289	biological_process	protein homotetramerization
D	0005509	molecular_function	calcium ion binding
D	0005829	cellular_component	cytosol
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006152	biological_process	purine nucleoside catabolic process
D	0006206	biological_process	pyrimidine nucleobase metabolic process
D	0008477	molecular_function	purine nucleosidase activity
D	0016798	molecular_function	hydrolase activity, acting on glycosyl bonds
D	0016799	molecular_function	hydrolase activity, hydrolyzing N-glycosyl compounds
D	0032991	cellular_component	protein-containing complex
D	0042802	molecular_function	identical protein binding
D	0045437	molecular_function	uridine nucleosidase activity
D	0046133	biological_process	pyrimidine ribonucleoside catabolic process
D	0046872	molecular_function	metal ion binding
D	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
D	0051289	biological_process	protein homotetramerization

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CA A 400

Chain	Residue
A	ASP11
A	ASP16
A	ASP240
A	HOH502

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA B 400

Chain	Residue
B	ASP11
B	ASP16
B	ASN40
B	ASP240
B	HOH404

site_id	AC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA C 400

Chain	Residue
C	ASP11
C	ASP16
C	ASN40
C	ASP240
C	HOH433

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CA D 400

Chain	Residue
D	ASP11
D	ASP16
D	ASN40
D	ASP240
D	HOH417

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE NOS A 401

Chain	Residue
A	ASP15
A	ASP16
A	ASN40
A	ILE81
A	HIS82
A	MET150
A	ASN158
A	GLU164
A	PHE165
A	ASN166
A	GLN227
A	TYR231
A	HIS239
A	ASP240
A	HOH502

site_id	AC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE NOS B 401

Chain	Residue
B	ASP15
B	ASP16
B	ASN40
B	MET150
B	ASN158
B	GLU164
B	PHE165
B	ASN166
B	GLN227
B	TYR231
B	ASP240

site_id	AC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE NOS C 401

Chain	Residue
C	ASP15
C	ASP16
C	ASN40
C	ALA78
C	MET150
C	ASN158
C	GLU164
C	ASN166
C	ASP240

site_id	AC8
Number of Residues	15
Details	BINDING SITE FOR RESIDUE NOS D 401

Chain	Residue
D	ASP15
D	ASP16
D	ASN40
D	ALA78
D	ILE81
D	HIS82
D	MET150
D	ASN158
D	GLU164
D	PHE165
D	ASN166
D	GLN227
D	TYR231
D	ASP240
D	HOH417

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE TAM D 402

Chain	Residue
C	MET136
C	GLN137
D	LEU43
D	GLY66
D	PRO68
D	HIS103

Functional Information from PROSITE/UniProt

site_id	PS01247
Number of Residues	11
Details	IUNH Inosine-uridine preferring nucleoside hydrolase family signature. DcDPGhDDAIA

Chain	Residue	Details
A	ASP9-ALA19

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: Proton acceptor => ECO:0000255

Chain	Residue	Details
A	ASP11
B	ASP11
C	ASP11
D	ASP11

site_id	SWS_FT_FI2
Number of Residues	16
Details	BINDING:

Chain	Residue	Details
A	ASP11
C	ASP16
C	VAL124
C	ASP240
D	ASP11
D	ASP16
D	VAL124
D	ASP240
A	ASP16
A	VAL124
A	ASP240
B	ASP11
B	ASP16
B	VAL124
B	ASP240
C	ASP11

site_id	SWS_FT_FI3
Number of Residues	8
Details	BINDING: BINDING => ECO:0000250

Chain	Residue	Details
A	GLN227
A	HIS239
B	GLN227
B	HIS239
C	GLN227
C	HIS239
D	GLN227
D	HIS239

Catalytic Information from CSA

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

Chain	Residue	Details
A	ASN166
A	ASP11
A	HIS239

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

Chain	Residue	Details
B	ASN166
B	ASP11
B	HIS239

site_id	CSA3
Number of Residues	3
Details	Annotated By Reference To The Literature 1mas

Chain	Residue	Details
C	ASN166
C	ASP11
C	HIS239

site_id	CSA4
Number of Residues	3
Details	Annotated By Reference To The Literature 1mas

Chain	Residue	Details
D	ASN166
D	ASP11
D	HIS239

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