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The wild type crystal structure of B-1,4-xylanase (XYNAS9) with xylobiose from streptomyces sp. 9

Analyse The wild type crystal structure of B-1,4-xylanase (XYNAS9) with xylobiose from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3WUE
Type
protein
Length
312 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Endo-1,4-beta-xylanase a
EC
3.2.1.8
UniProt
B4XVN1
Ligands
XYP, ZN
Pockets
1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndo-1,4-beta-xylanase a (EC 3.2.1.8)protein31244% helix, 21% strandB4XVN1

Ligands and binding sites

  • XYP · beta-D-xylopyranose · sugar · 4 copies · chains A
  • ZN · Zinc ion · metal · 5 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11440.460.7726XYP

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 3WUE · The wild type crystal structure of b-1,4-Xylanase (XynAS9) with xylobiose from… · the same entry in another collection · chain A against A, TM-score 1.00
  • B4XVN1 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase a (B4XVN1) · a predicted model of the same protein · chain A against A, TM-score 1.00

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