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Structure of PDB 4wmk Chain A Binding Site BS05

Receptor Information
>4wmk Chain A (length=299) Species: 10090 (Mus musculus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVS
EEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFS
AGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFD
NFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVM
LLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPE
LFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPE
Ligand information
Ligand IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4wmk Chain A Residue 402 [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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PDB4wmk Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		M103 F104 T105 D225 L226 D227 N384 C385
Binding residue
(residue number reindexed from 1)		M11 F12 T13 D133 L134 D135 N292 C293
Annotation score3
Enzymatic activity
Enzyme Commision number 2.4.2.62: xylosyl alpha-1,3-xylosyltransferase.
Gene Ontology
Molecular Function
GO:0016757 glycosyltransferase activity
GO:0035252 UDP-xylosyltransferase activity

View graph for
Molecular Function
External links
PDB RCSB:4wmk, PDBe:4wmk, PDBj:4wmk
PDBsum4wmk
PubMed26414444
UniProtQ3U4G3|XXLT1_MOUSE Xyloside xylosyltransferase 1 (Gene Name=Xxylt1)

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