Structure of PDB 3g5i Chain C Binding Site BS02

Receptor Information

>3g5i Chain C (length=293) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]

ALPILLDCDPGHDDAIAIVLALASPELDVKAITSSAGNQTPEKTLRNVLR
MLTLLNRTDIPVAGGAVKPLMRELGLDGPALPEPTFAPQNCTAVELMAKT
LRESAEPVTIVSTGPQTNVALLLNSHPELHSKIARIVIMGGAMGLGNWTP
AAEFNIYVDPEAAEIVFQSGIPVVMAGLDVTHKAQIHVEDTERFRAIGNP
VSTIVAELLDFEKWGFVGAPLHDPCTIAWLLKPELFTSVERWVGVETQGK
YTQGMTVVDYYYLTGNKPNATVMVDVDRQGFVDLLADRLKFYA

Ligand information

Ligand ID

DNB

InChI

InChI=1S/C11H17N3O3/c12-6-2-1-5(3-7(6)13)9-11(17)10(16)8(4-15)14-9/h1-3,8-11,14-17H,4,12-13H2/t8-,9+,10-,11+/m1/s1

InChIKey

YAYMFJWCRXEXGZ-YTWAJWBKSA-N

SMILES

Software	SMILES
OpenEye OEToolkits 1.5.0	c1cc(c(cc1[C@H]2[C@@H]([C@@H]([C@H](N2)CO)O)O)N)N
OpenEye OEToolkits 1.5.0	c1cc(c(cc1C2C(C(C(N2)CO)O)O)N)N
CACTVS 3.341	Nc1ccc(cc1N)[C@@H]2N[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04	OC2C(c1ccc(N)c(N)c1)NC(CO)C2O
CACTVS 3.341	Nc1ccc(cc1N)[CH]2N[CH](CO)[CH](O)[CH]2O

Formula

C11 H17 N3 O3

Name

(2S,3S,4R,5R)-2-(3,4-diaminophenyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol;
Diaminophenyl iminoribitol

PDB chain

3g5i Chain C Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure

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Structure summary

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PDB	3g5i Active site plasticity revealed from the structure of the enterobacterial N-ribohydrolase RihA bound to a competitive inhibitor.
Resolution	2.1 Å
Binding residue (original residue number in PDB)	D14 N39 M150 E164 N166 D241
Binding residue (residue number reindexed from 1)	D13 N38 M139 E153 N155 D223
Annotation score	1

Enzymatic activity

Catalytic site (original residue number in PDB)	D10 D15 N39 L75 T124 F165 N166 H240 D241
Catalytic site (residue number reindexed from 1)	D9 D14 N38 L74 T113 F154 N155 H222 D223
Enzyme Commision number	3.2.-.-

Gene Ontology

	Molecular Function
GO:0005509	calcium ion binding
GO:0005515	protein binding
GO:0008477	purine nucleosidase activity
GO:0016798	hydrolase activity, acting on glycosyl bonds
GO:0016799	hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0042802	identical protein binding
GO:0045437	uridine nucleosidase activity
GO:0050263	ribosylpyrimidine nucleosidase activity

	Biological Process
GO:0006139	nucleobase-containing compound metabolic process
GO:0006152	purine nucleoside catabolic process
GO:0006206	pyrimidine nucleobase metabolic process
GO:0015949	nucleobase-containing small molecule interconversion
GO:0046133	pyrimidine ribonucleoside catabolic process
GO:0051289	protein homotetramerization

	Cellular Component
GO:0005829	cytosol
GO:0032991	protein-containing complex

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Cellular Component

External links

PDB	RCSB:3g5i, PDBe:3g5i, PDBj:3g5i
PDBsum	3g5i
PubMed	20529317
UniProt	P41409\|RIHA_ECOLI Pyrimidine-specific ribonucleoside hydrolase RihA (Gene Name=rihA)

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