Structure of PDB 5ify Chain F Binding Site BS01

Receptor Information
>5ify Chain F (length=292) 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
CPEEIAYRRNWIDAEQVLKLAQPLAKNAYGQYLRNLLTHQVA
Ligand information
Ligand IDTRH
InChIInChI=1S/C16H26N2O15P2/c1-6-4-18(16(24)17-14(6)23)10-3-8(19)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)12(21)11(20)7(2)30-15/h4,7-13,15,19-22H,3,5H2,1-2H3,(H,25,26)(H,27,28)(H,17,23,24)/t7-,8-,9+,10+,11-,12+,13+,15+/m0/s1
InChIKeyZOSQFDVXNQFKBY-CGAXJHMRSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
CACTVS 3.341C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](O)[CH]1O
CACTVS 3.341C[C@@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@H](O)[C@H]1O
ACDLabs 10.04O=P(OC1OC(C(O)C(O)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O
OpenEye OEToolkits 1.5.0C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)O)O
FormulaC16 H26 N2 O15 P2
Name2'-DEOXY-THYMIDINE-BETA-L-RHAMNOSE
ChEMBL
DrugBankDB03723
ZINCZINC000008218444
PDB chain5ify Chain F Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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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)		L8 G10 S12 Q82 P85 G87 L88 L108 D110 Y145 G146 E161 K162 V172 G174 Y176 R194
Binding residue
(residue number reindexed from 1)		L7 G9 S11 Q81 P84 G86 L87 L107 D109 Y144 G145 E160 K161 V171 G173 Y175 R193
Annotation score3
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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