Structure of PDB 4wmk Chain A Binding Site BS03

Receptor Information

>4wmk Chain A (length=299) Species: 10090 (Mus musculus)

VVPVDYHLLMMFTKAEHNAPLQAKARVALSSLLRLAKFEAHEVLNLHFVS
EEASREVAKALLRELLPPAAGFKCKVIFHDVAVLTDKLFPVVEAMQKYFS
AGSGTYYSDSIFFLSVAMHQIMPKEIPRIIQLDLDLKYKTNIRELFEEFD
NFLPGAVIGIAREMQPVYRHTFWQFRHENPKTRVGDPPPEGLPGFNSGVM
LLNLEAMRQSPLYSHLLEPSWVQQLADKYHFRGHLGDQDFFTMIGMEHPE
LFHVLDCTWNRQLCTWWRDHGYSDVFQAYFRCEGHVKIYHGNCNTPIPE

Ligand information

• Ligand ID: XYS
• InChI: InChI=1S/C5H10O5/c6-2-1-10-5(9)4(8)3(2)7/h2-9H,1H2/t2-,3+,4-,5+/m1/s1
• InChIKey: SRBFZHDQGSBBOR-LECHCGJUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: O[CH]1CO[CH](O)[CH](O)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O
  CACTVS 3.341: O[C@@H]1CO[C@H](O)[C@H](O)[C@H]1O
  ACDLabs 10.04: OC1C(O)COC(O)C1O
• Formula: C5 H10 O5
• Name: alpha-D-xylopyranose;
  alpha-D-xylose;
  D-xylose;
  xylose;
  XYLOPYRANOSE
• DrugBank: DB03389
• ZINC: ZINC000001529214
• PDB chain: 4wmk Chain B Residue 3

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4wmk Notch-modifying xylosyltransferase structures support an SNi-like retaining mechanism.
• Resolution: 2.08 Å
• Binding residue (original residue number in PDB): D225 N288 S289 G290 Q330 H382
• Binding residue (residue number reindexed from 1): D133 N196 S197 G198 Q238 H290
• Annotation score: 1

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