› 2z6w

X-ray diffraction
0.96Å resolution

Crystal structure of human cyclophilin D in complex with cyclosporin A

Released:
DOI: 10.2210/pdb2z6w/pdb
PDB entry 2z6w coloured by chain, front view.
PDB entry 2z6w coloured by chain, side view.
PDB entry 2z6w coloured by chain, top view.
Source organisms:
Primary publication:
Crystal structure of human cyclophilin D in complex with its inhibitor, cyclosporin A at 0.96-A resolution.
Kajitani K, Fujihashi M, Kobayashi Y, Shimizu S, Tsujimoto Y, Miki K
Proteins 70 1635-9 (2008)
PMID: 18076075

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151716 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Peptidyl-prolyl cis-trans isomerase F, mitochondrial Chains: A, B
Molecule details ›
Chains: A, B
Length: 165 amino acids
Theoretical weight: 17.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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
CYCLOSPORIN A Chains: M, N
Molecule details ›
Chains: M, N
Length: 11 amino acids
Theoretical weight: 1.22 KDa
Source organism: Tolypocladium inflatum
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand CIT 1 x CIT
6 modified residues:
Ligand DAL 2 x DAL
Ligand MLE 8 x MLE
Ligand MVA 2 x MVA
Ligand BMT 2 x BMT
Ligand ABA 2 x ABA
Ligand SAR 2 x SAR

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 38.882Å b: 69.313Å c: 112.077Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.13 0.129 0.153
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

Physiologic functions of cyclophilin D and the mitochondrial permeability transition pore.
Elrod et al. (2013)
4 more

13 mentions without citation

Non-Immunosuppressive Cyclophilin Inhibitors.
Schiene-Fischer et al. (2022)
12 more