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Emericilla nidulans endo-beta-1,4-galactanase

Analyse Emericilla nidulans endo-beta-1,4-galactanase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4BF7
Type
protein
Length
335 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Arabinogalactan endo-1,4-beta-galactosidase a
EC
3.2.1.89
UniProt
Q5B153
Ligands
NAG, ZN
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AArabinogalactan endo-1,4-beta-galactosidase a (EC 3.2.1.89)protein33538% helix, 16% strandQ5B153

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
  • ZN · Zinc ion · metal · 15 copies · chains A
  • ACT · Acetate ion · additive · 11 copies · chains A
  • IMD · Imidazole · additive · chains A
  • GOL · Glycerol · additive · 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
11730.510.7829ZN, ACT, GOL

Modifications

Observed in the structure: 1 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

  • 4BF7 · Emericilla nidulans endo-beta-1,4-galactanase · the same entry in another collection · chain A against A, TM-score 1.00
  • Q5B153 · AlphaFold monomer V2.0 prediction for arabinogalactan endo- beta-1,4-galactanase a… · a predicted model of the same protein · chain A against A, TM-score 0.99

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