Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3G5I

Crystal Structure of the E.coli RihA pyrimidine nucleosidase bound to a iminoribitol-based inhibitor

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005509	molecular_function	calcium ion binding
A	0005515	molecular_function	protein 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	0015949	biological_process	nucleobase-containing small molecule interconversion
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	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
A	0051289	biological_process	protein homotetramerization
B	0005509	molecular_function	calcium ion binding
B	0005515	molecular_function	protein 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	0015949	biological_process	nucleobase-containing small molecule interconversion
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	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
B	0051289	biological_process	protein homotetramerization
C	0005509	molecular_function	calcium ion binding
C	0005515	molecular_function	protein 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	0015949	biological_process	nucleobase-containing small molecule interconversion
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	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
C	0051289	biological_process	protein homotetramerization
D	0005509	molecular_function	calcium ion binding
D	0005515	molecular_function	protein 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	0015949	biological_process	nucleobase-containing small molecule interconversion
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	0050263	molecular_function	ribosylpyrimidine nucleosidase activity
D	0051289	biological_process	protein homotetramerization

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE BME A 1102

Chain	Residue
A	GLN100
A	CYS102
A	LEU107
A	LYS110
C	GLU114

site_id	AC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA A 501

Chain	Residue
A	ASP241
A	HOH312
A	DNB502
A	ASP10
A	ASP15
A	ASN39
A	THR124

site_id	AC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE DNB A 502

Chain	Residue
A	ASP14
A	ASP15
A	ASN39
A	VAL81
A	HIS82
A	THR124
A	MET150
A	ASN158
A	GLU164
A	ASN166
A	ASP241
A	HOH312
A	CA501

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA B 501

Chain	Residue
B	ASP10
B	ASP15
B	ASN39
B	THR124
B	ASP241
B	HOH455
B	DNB502

site_id	AC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DNB B 502

Chain	Residue
B	ASP14
B	ASP15
B	ASN39
B	THR124
B	MET150
B	ASN158
B	TRP159
B	GLU164
B	ASN166
B	ASP241
B	HOH455
B	CA501

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA C 501

Chain	Residue
C	ASP10
C	ASP15
C	ASN39
C	THR124
C	ASP241
C	DNB502
C	HOH573

site_id	AC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DNB C 502

Chain	Residue
C	ASP14
C	ASP15
C	ASN39
C	THR124
C	MET150
C	ASN158
C	GLU164
C	PHE165
C	ASN166
C	ASP241
C	CA501
C	HOH573

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE CA D 501

Chain	Residue
D	ASP10
D	ASP15
D	ASN39
D	THR124
D	ASP241
D	HOH390
D	DNB502

site_id	AC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE DNB D 502

Chain	Residue
D	ASP14
D	ASP15
D	ASN39
D	THR124
D	MET150
D	ASN158
D	TRP159
D	GLU164
D	ASN166
D	ASP241
D	HOH390
D	CA501

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	ASP8-ALA18

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	ACT_SITE: ACT_SITE => ECO:0000250

Chain	Residue	Details
A	HIS240
B	HIS240
C	HIS240
D	HIS240

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