Structure of PDB 4r2w Chain F Binding Site BS03

Receptor Information
>4r2w Chain F (length=242) Species: 211586 (Shewanella oneidensis MR-1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ADVFHLGLTKAMLDGATLAIVPGDPERVKRIAELMDNATFLASHREYTSY
LAYADGKPVVICSTGIGGPSTSIAVEELAQLGVNTFLRVGTTGAIQPHVN
VGDVIVTQASVRLDGASLHFAPMEFPAVANFECTTAMVAACRDAGVEPHI
GVTASSDTFYPGQERYDTVTGRVTRRFAGSMKEWQDMGVLNYEMESATLF
TMCATQGWRAACVAGVIVNRTQQEIPVSAVSIVVAAAKKLLA
Ligand information
Ligand IDGOL
InChIInChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
InChIKeyPEDCQBHIVMGVHV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C(C(CO)O)O
ACDLabs 12.01
CACTVS 3.370		OCC(O)CO
FormulaC3 H8 O3
NameGLYCEROL;
GLYCERIN;
PROPANE-1,2,3-TRIOL
ChEMBLCHEMBL692
DrugBankDB09462
ZINCZINC000000895048
PDB chain4r2w Chain F Residue 304 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4r2w High-syn conformation of uridine and asymmetry of the hexameric molecule revealed in the high-resolution structures of Shewanella oneidensis MR-1 uridine phosphorylase in the free form and in complex with uridine.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		N130 A204
Binding residue
(residue number reindexed from 1)		N130 A204
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H5 G23 R27 R45 E77 R88 T91 R165 I217 V218 R220
Catalytic site (residue number reindexed from 1) H5 G23 R27 R45 E77 R88 T91 R165 I217 V218 R220
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: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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4r2w, PDBe:4r2w, PDBj:4r2w
PDBsum4r2w
PubMed25478848
UniProtQ8E9X9

[Back to BioLiP]