Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1Q8F

Crystal Structure of the E.coli pyrimidine nucleoside hydrolase yeiK

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	7
Details	BINDING SITE FOR RESIDUE CA A 2001

Chain	Residue
A	ASP11
A	ASP16
A	VAL124
A	ASP240
A	GOL3001
A	HOH3022
A	HOH3026

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA B 2002

Chain	Residue
B	VAL124
B	ASP240
B	GOL3002
B	HOH3028
B	HOH3041
B	ASP11
B	ASP16

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA C 2003

Chain	Residue
C	ASP11
C	ASP16
C	VAL124
C	ASP240
C	GOL3003
C	HOH3027
C	HOH3047

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA D 2004

Chain	Residue
D	ASP11
D	ASP16
D	VAL124
D	ASP240
D	GOL3004
D	HOH3023
D	HOH3039

site_id	AC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GOL A 3001

Chain	Residue
A	ASP15
A	VAL124
A	MET150
A	ASN158
A	GLU164
A	PHE165
A	ASN166
A	ASP240
A	CA2001
A	GOL3005
A	HOH3022
A	HOH3026

site_id	AC6
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GOL B 3002

Chain	Residue
B	ASP15
B	VAL124
B	MET150
B	ASN158
B	GLU164
B	PHE165
B	ASN166
B	HIS239
B	ASP240
B	CA2002
B	GOL3006
B	HOH3028
B	HOH3041

site_id	AC7
Number of Residues	13
Details	BINDING SITE FOR RESIDUE GOL C 3003

Chain	Residue
C	ASP15
C	VAL124
C	MET150
C	ASN158
C	GLU164
C	PHE165
C	ASN166
C	ASP240
C	CA2003
C	GOL3007
C	HOH3027
C	HOH3047
C	HOH3071

site_id	AC8
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GOL D 3004

Chain	Residue
D	ASP15
D	VAL124
D	MET150
D	ASN158
D	GLU164
D	PHE165
D	ASN166
D	ASP240
D	CA2004
D	GOL3008
D	HOH3023
D	HOH3039

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 3005

Chain	Residue
A	ASN40
A	ALA78
A	HIS82
A	ASN158
A	PHE159
A	PHE165
A	TYR231
A	GOL3001
A	HOH3095

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL B 3006

Chain	Residue
B	ASN40
B	ALA78
B	HIS82
B	ASN158
B	PHE159
B	PHE165
B	TYR231
B	GOL3002
B	HOH3067
B	HOH3088

site_id	BC2
Number of Residues	12
Details	BINDING SITE FOR RESIDUE GOL C 3007

Chain	Residue
C	ILE81
C	HIS82
C	ASN158
C	PHE159
C	PHE165
C	TYR231
C	GOL3003
C	HOH3071
C	HOH3158
C	HOH3282
C	ASN40
C	ALA78

site_id	BC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL D 3008

Chain	Residue
D	ASN40
D	ALA78
D	HIS82
D	ASN158
D	PHE159
D	PHE165
D	TYR231
D	GOL3004
D	HOH3108

site_id	BC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL A 3009

Chain	Residue
A	GLN74
A	GOL3015
A	HOH3274

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 3010

Chain	Residue
A	ARG135
A	VAL176
A	THR179
A	HOH3091
B	GOL3011

site_id	BC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL B 3011

Chain	Residue
A	ARG135
A	GOL3010
B	GLN69
B	PRO70
B	ARG73
B	GLN74
B	GLN75

site_id	BC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL C 3012

Chain	Residue
C	MET134
C	ARG135
C	VAL176
C	THR179
C	SER180
D	GLN74
D	GOL3014
D	HOH3050

site_id	BC8
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL D 3014

Chain	Residue
C	ARG135
C	GOL3012
D	GLN69
D	PRO70
D	ARG73
D	GLN74
D	GLN75
D	HOH3311

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL A 3015

Chain	Residue
A	GLN69
A	PRO70
A	ARG73
A	GLN74
A	GLN75
A	GOL3009
B	ARG135

site_id	CC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 3016

Chain	Residue
C	GLN69
C	PRO70
C	ARG73
C	GLN74
C	GLN75
C	HOH3298
D	ARG135
D	GOL3017
D	HOH3239

site_id	CC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL D 3017

Chain	Residue
C	GOL3016
D	ARG135
D	VAL176
D	THR179
D	HOH3040
D	HOH3109

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
A	ASP16
D	ASP11
D	ASP16
D	VAL124
D	ASP240
A	VAL124
A	ASP240
B	ASP11
B	ASP16
B	VAL124
B	ASP240
C	ASP11
C	ASP16
C	VAL124
C	ASP240

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

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

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