Structure of PDB 7dfn Chain B Binding Site BS01

Receptor Information

>7dfn Chain B (length=194) Species: 1921 (Streptomyces olivaceoviridis)

ATVITTNQTGTNNGFYYSFWTDGGGSVSMTLNSGGNYSTSWTNCGNFVAG
KGWSNGGRRNVQYSGSFYPSGNGYLALYGWTSNPLVEYYIVDNWGNYRPT
GTYKGTVTSDGGTYDVYQTTRYNAPSVEGTKTFNQYWSVRQSKRTGGTIT
TGNHFDAWARYGMQLGSFSYYMILATEGYQSSGSSNLTVSGKLA

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: 7dfn Chain F Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7dfn Structure-based substrate specificity analysis of GH11 xylanase from Streptomyces olivaceoviridis E-86.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): W20 N46 V48 Y78 E87 R121 P125 E177
• Binding residue (residue number reindexed from 1): W20 N46 V48 Y78 E87 R121 P125 E177
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N46 Y78 E87 Y89 E177
• Catalytic site (residue number reindexed from 1): N46 Y78 E87 Y89 E177
• Enzyme Commision number: 3.2.1.8: endo-1,4-beta-xylanase.

Gene Ontology

Molecular Function

• GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds
• GO:0016798 hydrolase activity, acting on glycosyl bonds
• GO:0031176 endo-1,4-beta-xylanase activity

Biological Process

• GO:0005975 carbohydrate metabolic process
• GO:0045493 xylan catabolic process

External links

• PDB: RCSB:7dfn, PDBe:7dfn, PDBj:7dfn
• PDBsum: 7dfn
• PubMed: 33564921
• UniProt: A0A7G1MBT0