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Hydrogen bonding and catalysis: an unexpected explanation for how a single amino acid substitution can change the pH optimum of a glycosidase

Analyse Hydrogen bonding and catalysis: an unexpected explanation for how a single… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
1C5I
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 0.47

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 62% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AEndo-1,4-beta-xylanase (EC 3.2.1.8)protein1855% helix, 62% 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11410.470.7826DFX, XYP

Modifications

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

Compared structures

  • 1C5I · Hydrogen bonding and catalysis: an unexpected explanation for how a single amino acid… · 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

Analyse

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