Structure of PDB 3kvv Chain C Binding Site BS03

Receptor Information
>3kvv Chain C (length=241) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDVFHLGLTKNDLQGATLAIVPGDPDRVEKIAALMDKPVKLASHREFTTW
RAELDGKPVIVCSTGIGGPSTSIAVEELAQLGIRTFLRIGTTGAIQPHIN
VGDVLVTTASVRLDGASLHFAPLEFPAVADFECTTALVEAAKSIGATTHV
GVTASSDTFYPGQERYDTYSGRVVRHFKGSMEEWQAMGVMNYEMESATLL
TMCASQGLRAGMVAGVIVNRTQKQTESHAVKIVVEAARRLL
Ligand information
Ligand IDR2B
InChIInChI=1S/C5H8O4/c6-1-4-5(8)3(7)2-9-4/h2,4-8H,1H2/t4-,5+/m1/s1
InChIKeyWGCMRWDTTZWXPL-UHNVWZDZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=C(C(C(O1)CO)O)O
OpenEye OEToolkits 1.7.0C1=C([C@@H]([C@H](O1)CO)O)O
ACDLabs 12.01OC1=COC(CO)C1O
CACTVS 3.370OC[CH]1OC=C(O)[CH]1O
CACTVS 3.370OC[C@H]1OC=C(O)[C@@H]1O
FormulaC5 H8 O4
Name1,4-anhydro-D-erythro-pent-1-enitol
ChEMBL
DrugBank
ZINCZINC000103554899
PDB chain3kvv Chain C Residue 256 [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]
PDB3kvv Glycal formation in crystals of uridine phosphorylase.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		T94 E196 M197 E198
Binding residue
(residue number reindexed from 1)		T91 E193 M194 E195
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) H8 G26 R30 R48 E80 R91 T94 R168 I220 V221 R223
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:0005524 ATP binding
GO:0016757 glycosyltransferase activity
GO:0016763 pentosyltransferase activity
GO:0030955 potassium ion binding
GO:0042802 identical protein binding
GO:0047847 deoxyuridine phosphorylase activity
Biological Process
GO:0006218 uridine catabolic process
GO:0006974 DNA damage response
GO:0009116 nucleoside metabolic process
GO:0009164 nucleoside catabolic process
GO:0009166 nucleotide catabolic process
GO:0044206 UMP salvage
GO:0046050 UMP catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0032991 protein-containing complex

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3kvv, PDBe:3kvv, PDBj:3kvv
PDBsum3kvv
PubMed20364833
UniProtP12758|UDP_ECOLI Uridine phosphorylase (Gene Name=udp)

[Back to BioLiP]