Structure of PDB 8y1m Chain B Binding Site BS03

Receptor Information

>8y1m Chain B (length=358) Species: 502601 (Bacillus sp. TAR1)

DQPFAWQVASLSERYQEQFDIGAAVEPYQLEGRQAQILKHHYNSLVAENA
MKPESLQPREGEWNWEGADKIVEFARKHNMELRFHTLVWHSQVPEWFFID
EDGNRMVDETDPDKREANKQLLLERMENHIKTVVERYKDDVTSWDVVNEV
IDDGGGLRESEWYQITGTDYIKVAFETARKYGGEEAKLYINDYNTEVPSK
RDDLYNLVKDLLEQGVPIDGVGHQSHIQIGWPSIEDTRASFEKFTSLGLD
NQVTELDMSLYGWPPTGAYTSYDDIPAELLQAQADRYDQLFELYEELAAD
ISSVTFWGIADNHTWLDGRAREYNNGVGIDAPFVFDHNYRVKPAYWRIID
LEHHHHHH

Ligand information

• Ligand ID: XYP
• 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-KKQCNMDGSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: C1C(C(C(C(O1)O)O)O)O
  CACTVS 3.341: O[C@@H]1CO[C@@H](O)[C@H](O)[C@H]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)O)O
  CACTVS 3.341: O[CH]1CO[CH](O)[CH](O)[CH]1O
  ACDLabs 10.04: OC1C(O)COC(O)C1O
• Formula: C5 H10 O5
• Name: beta-D-xylopyranose;
  beta-D-xylose;
  D-xylose;
  xylose
• ZINC: ZINC000001529215
• PDB chain: 8y1m Chain F Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8y1m Activity-stability trade-off observed in variants at position 315 of the GH10 xylanase XynR.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y194 N195 W264 R320
• Binding residue (residue number reindexed from 1): Y193 N194 W263 R319
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.2.1.8: endo-1,4-beta-xylanase.

Gene Ontology

Molecular Function

• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0031176 endo-1,4-beta-xylanase activity

Biological Process

• GO:0045493 xylan catabolic process

Cellular Component

• GO:0005576 extracellular region

External links

• PDB: RCSB:8y1m, PDBe:8y1m, PDBj:8y1m
• PDBsum: 8y1m
• PubMed: 38565938
• UniProt: P07528|XYNA_HALH5 Endo-1,4-beta-xylanase A (Gene Name=xynA)