› 7thf

X-ray diffraction
1.1Å resolution

Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B53

Released:
DOI: 10.2210/pdb7thf/pdb
PDB entry 7thf coloured by chain, front view.
PDB entry 7thf coloured by chain, side view.
PDB entry 7thf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery and molecular basis of subtype-selective cyclophilin inhibitors.
Peterson AA, Rangwala AM, Thakur MK, Ward PS, Hung C, Outhwaite IR, Chan AI, Usanov DL, Mootha VK, Seeliger MA, Liu DR
OpenAccess logo Nat Chem Biol (2022)
PMID: 36163383

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 BL21(DE3)
UniProt:
  • Canonical: P30405 (Residues: 44-207; Coverage: 79%)
Gene names: CYP3, PPIF
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD

Ligands and Environments

1 bound ligand:
Ligand I4R 1 x I4R
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS-II BEAMLINE 17-ID-1
Unit cell:
a: 38.492Å b: 66.885Å c: 68.968Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.137 0.137 0.148
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Mitochondria in health, disease, and aging.
Harrington et al. (2023)
4 more

3 mentions without citation

SULT1A3-mediated regiospecific 7-O-sulfation of flavonoids in Caco-2 cells can be explained by the relevant molecular docking studies.
Meng et al. (2012)
2 more