› 5p2m

X-ray diffraction
1.09Å resolution

Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 140

Released:
DOI: 10.2210/pdb5p2m/pdb
PDB entry 5p2m coloured by chain, front view.
PDB entry 5p2m coloured by chain, side view.
PDB entry 5p2m coloured by chain, top view.
Source organism: Cryphonectria parasitica
Primary publication:
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
Schiebel J, Krimmer SG, Röwer K, Knörlein A, Wang X, Park AY, Stieler M, Ehrmann FR, Fu K, Radeva N, Krug M, Huschmann FU, Glöckner S, Weiss MS, Mueller U, Klebe G, Heine A
Structure 24 1398-1409 (2016)
PMID: 27452405

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

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.3
Spacegroup: P21
Unit cell:
a: 45.284Å b: 72.915Å c: 52.737Å
α: 90° β: 109.48° γ: 90°
R-values:
R R work R free
0.134 0.133 0.148

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Citations

7 review citations

Current perspectives in fragment-based lead discovery (FBLD).
Lamoree et al. (2017)
6 more