Structure of PDB 3vpl Chain A Binding Site BS01

Receptor Information

>3vpl Chain A (length=324) Species: 678 (Vibrio sp.)

LDGVLVPESGILVSVGQDVDSVNDYASALGTIPAGVTNYVGIVNLDGLNS
DADAGAGRNNIAELANAYPTSALVVGVSMNGEVDAVASGRYNANIDTLLN
TLAGYDRPVYLRWAYEVDGPWNGHSPSGIVTSFQYVHDRIIALGHQAKIS
LVWQVASYCPTPGGQLDQWWPGSEYVDWVGLSYFAPQDCNWDRVNEAAQF
ARSKGKPLFLNESTPQRYQVADLTYSADPAKGTNRQSKTSQQLWDEWFAP
YFQFMSDNSDIVKGFTYINADWDSQWRWAAPYNEGYWGDSRVQANALIKS
NWQQEIAKGQYINHSETLFETLGY

Ligand information

• Ligand ID: BXF
• InChI: InChI=1S/C5H9FO4/c6-3-4(8)2(7)1-10-5(3)9/h2-5,7-9H,1H2/t2-,3-,4+,5-/m1/s1
• InChIKey: YVMHSZGJGHRGOD-SQOUGZDYSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: C1[C@H]([C@@H]([C@H]([C@@H](O1)O)F)O)O
  CACTVS 3.370: O[C@@H]1CO[C@@H](O)[C@H](F)[C@H]1O
  CACTVS 3.370: O[CH]1CO[CH](O)[CH](F)[CH]1O
  OpenEye OEToolkits 1.7.6: C1C(C(C(C(O1)O)F)O)O
  ACDLabs 12.01: FC1C(O)C(O)COC1O
• Formula: C5 H9 F O4
• Name: 2-deoxy-2-fluoro-beta-D-xylopyranose;
  2-deoxy-2-fluoro-beta-D-xylose;
  2-deoxy-2-fluoro-D-xylose;
  2-deoxy-2-fluoro-xylose
• PDB chain: 3vpl Chain B Residue 1

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3vpl Mechanistic insights into the 1,3-xylanases: useful enzymes for manipulation of algal biomass
• Resolution: 1.2 Å
• Binding residue (original residue number in PDB): Y115 E116 F184 E212 W272 W287
• Binding residue (residue number reindexed from 1): Y115 E116 F184 E212 W272 W287
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 3.2.1.32: endo-1,3-beta-xylanase.

Gene Ontology

Molecular Function

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

External links

• PDB: RCSB:3vpl, PDBe:3vpl, PDBj:3vpl
• PDBsum: 3vpl
• UniProt: D5MP61|3XYN1_VIBSX Beta-1,3-xylanase XYL4 (Gene Name=xyl4)