Structure of PDB 5ify Chain D Binding Site BS01

Receptor Information
>5ify Chain D (length=293) Species: 269482 (Burkholderia vietnamiensis G4) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ARKGIILAGGSGTRLYPITHAVSKQLLPVYDKPMIYYPLSTLMIAGIRDV
LIISTPQDTPRFESMLGDGSQWGMNIQYATQPSPDGLAQAFVIGRDFVGN
EPSALILGDNIFYGHDLAKQLERASAKDTGATVFAYHVQDPERYGVVEFD
REFRAISIEEKPAKPRSSYAVTGLYFYDRQVCDIAADIKPSARGELEITD
VNSRYLAAGQLDVELMGRGYAWLDTGTHDSLIEAGTFIATLQKRQGLMVA
CPEEIAYRRNWIDAEQVLKLAQPLAKNAYGQYLRNLLTHQVAW
Ligand information
Ligand IDUMP
InChIInChI=1S/C9H13N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,17)/t5-,6+,8+/m0/s1
InChIKeyJSRLJPSBLDHEIO-SHYZEUOFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)CC2O
CACTVS 3.370O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
CACTVS 3.370O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.6C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O
FormulaC9 H13 N2 O8 P
Name2'-DEOXYURIDINE 5'-MONOPHOSPHATE;
DUMP
ChEMBLCHEMBL211312
DrugBankDB03800
ZINCZINC000004228260
PDB chain5ify Chain C Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ify Crystal structure of Glucose-1-phosphate thymidylyltransferase from Burkholderia vietnamiensis in complex with 2'-Deoxyuridine-5'-monophosphate and 2'-Deoxy-Thymidine-B-L-Rhamnose
Resolution2.25 Å
Binding residue
(original residue number in PDB)		G218 R219 G220
Binding residue
(residue number reindexed from 1)		G217 R218 G219
Annotation score2
Enzymatic activity
Enzyme Commision number 2.7.7.24: glucose-1-phosphate thymidylyltransferase.
Gene Ontology
Molecular Function
GO:0008879 glucose-1-phosphate thymidylyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0009058 biosynthetic process
GO:0045226 extracellular polysaccharide biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5ify, PDBe:5ify, PDBj:5ify
PDBsum5ify
PubMed
UniProtA4JC15

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