› 6ybm

X-ray diffraction
1.41Å resolution

Scaffold-ligand complex with ligand unmodelled.

Released:
DOI: 10.2210/pdb6ybm/pdb
PDB entry 6ybm coloured by chain, front view.
PDB entry 6ybm coloured by chain, side view.
PDB entry 6ybm coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Zacharchenko T, Lian LY

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:
homo trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-151718 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidyl-prolyl cis-trans isomerase F, mitochondrial Chains: A, B, C
Molecule details ›
Chains: A, B, C
Length: 165 amino acids
Theoretical weight: 17.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
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

2 bound ligands:
Ligand EDO 3 x EDO
Ligand CIT 1 x CIT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: C2
Unit cell:
a: 125.521Å b: 58.635Å c: 103.293Å
α: 90° β: 124.852° γ: 90°
R-values:
R R work R free
0.18 0.178 0.211
Expression system: Homo sapiens

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