Structure of PDB 1bvv Chain A Binding Site BS01

Receptor Information

>1bvv Chain A (length=185) Species: 1397 (Niallia circulans)

ASTDYWQNWTDGGGIVNAVNGSGGNYSVNWSNTGNFVVGKGWTTGSPFRT
INYNAGVWAPNGNGYLTLYGWTRSPLIEYYVVDSWGTYRPTGTYKGTVKS
DGGTYDIYTTTRYNAPSIDGDRTTFTQYWSVRQSKRPTGSNATITFTNHV
NAWKSHGMNLGSNWAYQVMATEGYQSSGSSNVTVW

Ligand information

• Ligand ID: DFX
• InChI: InChI=1S/C5H9FO3/c6-3-1-9-2-4(7)5(3)8/h3-5,7-8H,1-2H2/t3-,4+,5+/m0/s1
• InChIKey: YIJTWYXBSRZXRS-VPENINKCSA-N
• SMILES:
  CACTVS 3.341: O[C@@H]1COC[C@H](F)[C@H]1O
  ACDLabs 10.04: FC1COCC(O)C1O
  CACTVS 3.341: O[CH]1COC[CH](F)[CH]1O
  OpenEye OEToolkits 1.5.0: C1[C@H]([C@@H]([C@H](CO1)F)O)O
  OpenEye OEToolkits 1.5.0: C1C(C(C(CO1)F)O)O
• Formula: C5 H9 F O3
• Name: 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol;
  1,2-DEOXY-2-FLUORO-XYLOPYRANOSE
• ZINC: ZINC000015297146
• PDB chain: 1bvv Chain B Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1bvv Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): Y69 E78 R112 P116 F125
• Binding residue (residue number reindexed from 1): Y69 E78 R112 P116 F125
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): N35 Y69 E78 Y80 E172
• Catalytic site (residue number reindexed from 1): N35 Y69 E78 Y80 E172
• 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:1bvv, PDBe:1bvv, PDBj:1bvv
• PDBsum: 1bvv
• PubMed: 10220321
• UniProt: P09850|XYNA_NIACI Endo-1,4-beta-xylanase (Gene Name=xlnA)