› 4y4j

X-ray diffraction
1.03Å resolution

Endothiapepsin in complex with fragment B97

Released:
DOI: 10.2210/pdb4y4j/pdb
PDB entry 4y4j coloured by chain, front view.
PDB entry 4y4j coloured by chain, side view.
PDB entry 4y4j coloured by chain, top view.
Source organism: Cryphonectria parasitica
Primary publication:
Structures of endothiapepsin-fragment complexes from crystallographic fragment screening using a novel, diverse and affordable 96-compound fragment library.
Huschmann FU, Linnik J, Sparta K, Ühlein M, Wang X, Metz A, Schiebel J, Heine A, Klebe G, Weiss MS, Mueller U
Acta Crystallogr F Struct Biol Commun 72 346-55 (2016)
PMID: 27139825

Function and Biology Details

Reaction catalysed: 
Hydrolysis of proteins with specificity similar to that of pepsin A, prefers hydrophobic residues at P1 and P1', but does not cleave 14-Ala-|-Leu-15 in the B chain of insulin or Z-Glu-Tyr. Clots milk.
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145946 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Endothiapepsin Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 33.81 KDa
Source organism: Cryphonectria parasitica
UniProt:
  • Canonical: P11838 (Residues: 90-419; Coverage: 83%)
Gene names: EAPA, EPN-1
Sequence domains: Eukaryotic aspartyl protease
Structure domains: Acid Proteases

Ligands and Environments

4 bound ligands:
Ligand GOL 5 x GOL
Ligand ACT 2 x ACT
Ligand DMS 4 x DMS
Ligand LNR 1 x LNR
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 45.225Å b: 72.937Å c: 52.663Å
α: 90° β: 109.2° γ: 90°
R-values:
R R work R free
0.111 0.11 0.126

Quick links

Citations

1 review citation

Protein X-ray Crystallography and Drug Discovery.
Maveyraud et al. (2020)
17 other articles

2 mentions without citation

Fragment Hits: What do They Look Like and How do They Bind?
Giordanetto et al. (2019)
1 more