Structure of PDB 1rrv Chain B Binding Site BS02

Receptor Information
>1rrv Chain B (length=400) Species: 31958 (Amycolatopsis orientalis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRVLLSVCGTRGDVEIGVALADRLKALGVQTRMCAPPAAEERLAEVGVPH
VPVGLPQHMMLQEGMPPPPPEEEQRLAAMTVEMQFDAVPGAAEGCAAVVA
VGDLAAATGVRSVAEKLGLPFFYSVPSPVYLASPHLPPAYDEPTTPGVTD
IRVLWEERAARFADRYGPTLNRRRAEIGLPPVEDVFGYGHGERPLLAADP
VLAPLQPDVDAVQTGAWLLSDERPLPPELEAFLAAGSPPVHIGFGSSSGR
GIADAAKVAVEAIRAQGRRVILSRGWTELVLPDDRDDCFAIDEVNFQALF
RRVAAVIHHGSAGTEHVATRAGVPQLVIPRNTDQPYFAGRVAALGIGVAH
DGPTPTFESLSAALTTVLAPETRARAEAVAGMVLTDGAAAAADLVLAAVG
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 chain1rrv Chain B Residue 1004 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1rrv Crystal Structure of Vancosaminyltransferase Gtfd from the Vancomycin Biosynthetic Pathway: Interactions with Acceptor and Nucleotide Ligands
Resolution2.0 Å
Binding residue
(original residue number in PDB)		T10 R11 G12 E15 S246 E293 V294 F296 H309 S311 G313 T314
Binding residue
(residue number reindexed from 1)		T10 R11 G12 E15 S246 E293 V294 F296 H309 S311 G313 T314
Annotation score4
Enzymatic activity
Enzyme Commision number 2.4.1.322: devancosaminyl-vancomycin vancosaminetransferase.
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:1rrv, PDBe:1rrv, PDBj:1rrv
PDBsum1rrv
PubMed15122882
UniProtQ9AFC7|GTFD_AMYOR Devancosaminyl-vancomycin vancosaminetransferase (Gene Name=gtfD)

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