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Crystal structure of cratabl, a trypsin inhibitor from crataeva tapia

Analyse Crystal structure of cratabl, a trypsin inhibitor from crataeva tapia in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4IHZ
Type
protein
Length
328 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Cratabl
Ligands
NAG, BMA, FUC, SO4, CL
Pockets
1 · best druggability 0.34

Structure

x-ray diffraction · 1 distinct chain · 5% helix, 40% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BCratablprotein1645% helix, 40% strand—

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
  • BMA · beta-D-mannopyranose · sugar
  • FUC · alpha-L-fucopyranose · sugar
  • SO4 · Sulfate ion · ion · 3 copies · chains A, B
  • CL · Chloride ion · ion · 2 copies · chains A, B
  • GOL · Glycerol · additive · 3 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1840.340.7525empty

Interfaces

1 interface between chains.

  • A–B · 685 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, oxidation).

Compared structures

  • 4IHZ · Crystal structure of CrataBL, a trypsin inhibitor from Crataeva tapia · the same entry in another collection · chain A against A, TM-score 1.00

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