Structure of PDB 5efo Chain C Binding Site BS01

Receptor Information

>5efo Chain C (length=251) Species: 666 (Vibrio cholerae)

KTVFHLGVTEADLNGATLAIIPGDPARVQKIAELMDNPVFLASHREYTVY
RAELDGQSVVVCSTGIGGPSTSIAVEELAQLGVRTFLRVGTTGAIQPHVN
VGDMIVTTGSVRLDGASLHFAPMEFPAVPDFDVATAMKAAAQESGATVHM
GVTASSDTFYPGQERYDTFTGRVVRRFQGSMKEWQDMGVLNFEMESATLL
TMCASSGLKAGCVAGVIINRTQKEIPDHATLKETEARSIKVVVEAARKML
K

Ligand information

• Ligand ID: CYT
• InChI: InChI=1S/C4H5N3O/c5-3-1-2-6-4(8)7-3/h1-2H,(H3,5,6,7,8)
• InChIKey: OPTASPLRGRRNAP-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=C1N=CC=C(N)N1
  OpenEye OEToolkits 1.5.0: C1=C(NC(=O)N=C1)N
  CACTVS 3.341: NC1=CC=NC(=O)N1
• Formula: C4 H5 N3 O
• Name: 6-AMINOPYRIMIDIN-2(1H)-ONE;
  CYTOSINE
• ChEMBL: CHEMBL15913
• ZINC: ZINC000000895210
• PDB chain: 5efo Chain C Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5efo X-ray structure uridine phosphorylase from Vibrio cholerae in complex with uridine at 2.24 A resolution
• Resolution: 1.63 Å
• Binding residue (original residue number in PDB): F161 Q165
• Binding residue (residue number reindexed from 1): F159 Q163
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): H7 G25 R29 R47 E79 R90 T93 R167 I219 I220 R222 L233
• Catalytic site (residue number reindexed from 1): H5 G23 R27 R45 E77 R88 T91 R165 I217 I218 R220 L231
• Enzyme Commision number: 2.4.2.3: uridine phosphorylase.

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0004850 uridine phosphorylase activity
• GO:0016757 glycosyltransferase activity
• GO:0016763 pentosyltransferase activity
• GO:0046872 metal ion binding
• GO:0047847 deoxyuridine phosphorylase activity

Biological Process

• GO:0009116 nucleoside metabolic process
• GO:0009164 nucleoside catabolic process
• GO:0009166 nucleotide catabolic process
• GO:0044206 UMP salvage

Cellular Component

• GO:0005737 cytoplasm
• GO:0005829 cytosol

External links

• PDB: RCSB:5efo, PDBe:5efo, PDBj:5efo
• PDBsum: 5efo
• UniProt: Q9K4U1