Structure of PDB 5d9p Chain B Binding Site BS05

Receptor Information

>5d9p Chain B (length=347) Species: 77095 (Segatella bryantii)

TYMEESAQSAVDNFGLGFNLGNTLDANGCGTGKPVATYETFWGQPETTQD
MMTFLMQNGFNAVRIPVTWYEHMDAEGNVDEAWMMRVKAIVEYAMNAGLY
AIVNVHHDTAAGSGAWIKADTDVYAATKEKFKKLWTQIANALADYDQHLL
FEGYNEMLDGNNSWDEPQKASGYEALNNYAQDFVDAVRATGGNNATRNLI
VNTYAAAKGENVLNNFMLPTDAVNNHLIVQVHSYDPWNFFNTKTTWDSEC
HNTLTEIFSALSKKFTTIPYIIGEYGTHGESDISVSKSSPAEKIKLAADQ
AADMVKLAKDHHSATFYWMSIFDGSDRIQPQWSLPTVVEAMQEAYNN

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: 5d9p Chain F Residue 5

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d9p Structure-Function Analysis of a Mixed-linkage beta-Glucanase/Xyloglucanase from the Key Ruminal Bacteroidetes Prevotella bryantii B14.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): A212 A213 K214 H238 Y240 D241
• Binding residue (residue number reindexed from 1): A206 A207 K208 H232 Y234 D235
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds

Biological Process

• GO:0000272 polysaccharide catabolic process

External links

• PDB: RCSB:5d9p, PDBe:5d9p, PDBj:5d9p
• PDBsum: 5d9p
• PubMed: 26507654
• UniProt: O06842