› 4xnc

X-ray diffraction
2.23Å resolution

Crystal structure at room temperature of cyclophilin D in complex with an inhibitor

Released:
DOI: 10.2210/pdb4xnc/pdb
PDB entry 4xnc coloured by chain, front view.
PDB entry 4xnc coloured by chain, side view.
PDB entry 4xnc coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Combining 'dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.
Gelin M, Delfosse V, Allemand F, Hoh F, Sallaz-Damaz Y, Pirocchi M, Bourguet W, Ferrer JL, Labesse G, Guichou JF
Acta Crystallogr D Biol Crystallogr 71 1777-87 (2015)
PMID: 26249358

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151715 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidyl-prolyl cis-trans isomerase F, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 164 amino acids
Theoretical weight: 17.65 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P30405 (Residues: 44-207; Coverage: 79%)
Gene names: CYP3, PPIF
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like

Ligands and Environments

1 bound ligand:
Ligand EA4 1 x EA4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P41212
Unit cell:
a: 58Å b: 58Å c: 88.41Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.142 0.14 0.186
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Guidelines for the successful generation of protein-ligand complex crystals.
Müller I. (2017)
1 more

1 mention without citation

Peptidyl-Proline Isomerases (PPIases): Targets for Natural Products and Natural Product-Inspired Compounds.
Dunyak et al. (2016)