Structure of PDB 4wlz Chain B Binding Site BS02

Receptor Information

>4wlz Chain B (length=290) Species: 10090 (Mus musculus)

VDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVSEEA
SREVAKALLRELLFKCKVIFHDVAVLTDKLFPVVEAMQKYFSAGSGTYYS
DSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFDNFLPGAVI
GIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVMLLNLEAMR
QSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPELFHVLDCT
WNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIP

Ligand information

• Ligand ID: UDP
• InChI: InChI=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
• InChIKey: XCCTYIAWTASOJW-XVFCMESISA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: C1=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 3.370: O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
  CACTVS 3.370: O[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 1.7.0: C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
  ACDLabs 12.01: O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
• Formula: C9 H14 N2 O12 P2
• Name: URIDINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL130266
• DrugBank: DB03435
• ZINC: ZINC000004490939
• PDB chain: 4wlz Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wlz Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.
• Resolution: 3.03 Å
• Binding residue (original residue number in PDB): M103 T105 D225 L226 D227 N384
• Binding residue (residue number reindexed from 1): M8 T10 D125 L126 D127 N284
• Annotation score: 3

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

External links

• PDB: RCSB:4wlz, PDBe:4wlz, PDBj:4wlz
• PDBsum: 4wlz
• PubMed: 26414444
• UniProt: Q3U4G3|XXLT1_MOUSE Xyloside xylosyltransferase 1 (Gene Name=Xxylt1)