› 5nov

X-ray diffraction
2Å resolution

Structure of cyclophilin A in complex with hexahydropyrimidine-2-thione

Released:
DOI: 10.2210/pdb5nov/pdb
PDB entry 5nov coloured by chain, front view.
PDB entry 5nov coloured by chain, side view.
PDB entry 5nov coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pushing the Limits of Detection of Weak Binding Using Fragment-Based Drug Discovery: Identification of New Cyclophilin Binders.
Georgiou C, McNae I, Wear M, Ioannidis H, Michel J, Walkinshaw M
J Mol Biol 429 2556-2570 (2017)
PMID: 28673552

Function and Biology Details

Reaction catalysed: 
Peptidylproline (omega=180) = peptidylproline (omega=0)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-549123 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidyl-prolyl cis-trans isomerase A Chain: A
Molecule details ›
Chain: A
Length: 165 amino acids
Theoretical weight: 18.04 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62937 (Residues: 1-165; Coverage: 100%)
Gene names: CYPA, PPIA
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like

Ligands and Environments

1 bound ligand:
Ligand 93B 1 x 93B
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 40.98Å b: 52.16Å c: 88.56Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.206 0.265
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Non-Immunosuppressive Cyclophilin Inhibitors.
Schiene-Fischer et al. (2022)
7 other articles

1 mention without citation

Coarse-grain simulations on NMR conformational ensembles highlight functional residues in proteins.
Sacquin-Mora S. (2019)