Structure of PDB 1pn3 Chain A Binding Site BS02

Receptor Information
>1pn3 Chain A (length=391) Species: 31958 (Amycolatopsis orientalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLITGCGSRGDTEPLVALAARLRELGADARMCLPPDYVERCAEVGVPM
VPVGRAVRAGAREPGELPPGAAEVVTEVVAEWFDKVPAAIEGCDAVVTTG
LLPAAVAVRSMAEKLGIPYRYTVLSPDHLPSEQSQAERDMYNQGADRLFG
DAVNSHRASIGLPPVEHLYDYGYTDQPWLAADPVLSPLRPTDLGTVQTGA
WILPDERPLSAELEAFLAAGSTPVYVGFGSSSRPATADAAKMAIKAVRAS
GRRIVLSRGWADLVLPDDGADCFVVGEVNLQELFGRVAAAIHHDSAGTTL
LAMRAGIPQIVVRRVVDNVVEQAYHADRVAELGVGVAVDGPVPTIDSLSA
ALDTALAPEIRARATTVADTIRADGTTVAAQLLFDAVSLEK
Ligand information
Ligand IDTYD
InChIInChI=1S/C10H16N2O11P2/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(22-8)4-21-25(19,20)23-24(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,19,20)(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1
InChIKeyUJLXYODCHAELLY-XLPZGREQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)OP(=O)(O)O)O
OpenEye OEToolkits 1.5.0CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)O)O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C(=C1)C)CC2O
CACTVS 3.341CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
CACTVS 3.341CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P](O)(O)=O)O2)C(=O)NC1=O
FormulaC10 H16 N2 O11 P2
NameTHYMIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL259724
DrugBankDB03103
ZINCZINC000008215882
PDB chain1pn3 Chain A Residue 406 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1pn3 Structure of the Tdp-Epi-Vancosaminyltransferase Gtfa from the Chloroeremomycin Biosynthetic Pathway.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		S10 R11 G12 E15 S230 E277 V278 H293 S295 G297 T298 L301
Binding residue
(residue number reindexed from 1)		S10 R11 G12 E15 S230 E277 V278 H293 S295 G297 T298 L301
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.311: dTDP-epi-vancosaminyltransferase.
Gene Ontology
Molecular Function
GO:0008194 UDP-glycosyltransferase activity
GO:0016757 glycosyltransferase activity
GO:0016758 hexosyltransferase activity
Biological Process
GO:0005975 carbohydrate metabolic process
GO:0017000 antibiotic biosynthetic process
GO:0030259 lipid glycosylation
GO:0033072 vancomycin biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:1pn3, PDBe:1pn3, PDBj:1pn3
PDBsum1pn3
PubMed12874381
UniProtP96558|GTFA_AMYOR dTDP-epi-vancosaminyltransferase (Gene Name=gtfA)

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