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MolNFT v1 · #82846 · protein

Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) E172H mutant with GLU78 covalently bonded to 2-deoxy-2-fluoro- xylobiose

3VZM · Endo-1,4-beta-xylanase: “Crystal structure of the bacillus circulans endo-beta-(1,4)-xylanase (bcx) E172H mutant with GLU78 covalently…”. X-ray diffraction, 2 ligands (DFX, XYP), 1 pocket (best druggability 0.54). MolNFT v1 #82846…

PDB
3VZM
Type
protein
Length
185 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Endo-1,4-beta-xylanase
EC
3.2.1.8
UniProt
P09850
Ligands
DFX, XYP
Pockets
1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 61% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndo-1,4-beta-xylanase (EC 3.2.1.8)protein1855% helix, 61% strandP09850

Ligands and binding sites

  • DFX · 1,5-anhydro-2-deoxy-2-fluoro-D-xylitol · ligand · chains A
  • XYP · beta-D-xylopyranose · sugar · 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, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11610.540.8028DFX, XYP

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

  • 3VZM · Crystal structure of the Bacillus circulans endo-beta-(1,4)-xylanase (BcX) E172H mutant… · the same entry in another collection · chain A against A, TM-score 1.00
  • P09850 · AlphaFold monomer V2.0 prediction for endo-1,4-beta-xylanase (P09850) · a predicted model of the same protein · chain A against A, TM-score 0.99

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