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Crystal structure of beta-1,4-D-mannanase from cryptopygus antarcticus in complex with mannopentaose

Analyse Crystal structure of beta-1,4-D-mannanase from cryptopygus antarcticus in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4OOZ
Type
protein
Length
733 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Beta-1,4-mannanase
EC
3.2.1.78
UniProt
B4XC07
Ligands
BMA
Pockets
1 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 29% helix, 19% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
ABeta-1,4-mannanase (EC 3.2.1.78)protein36829% helix, 19% strandB4XC07
BBeta-1,4-mannanase (EC 3.2.1.78)protein36530% helix, 19% strandB4XC07

Ligands and binding sites

  • BMA · beta-D-mannopyranose · sugar · 20 copies · chains A, B

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
110250.780.8099BMA

Interfaces

1 interface between chains.

  • A–B · 629 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

  • 4OOZ · Crystal structure of beta-1,4-D-mannanase from Cryptopygus antarcticus in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
  • B4XC07 · AlphaFold monomer V2.0 prediction for mannan endo-1,4-beta- mannosidase (B4XC07) · a predicted model of the same protein · chain B against A, TM-score 0.99

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