PDB 4tot structure summary ‹ Protein Data Bank in Europe (PDBe) ‹ EMBL-EBI

X-ray diffraction

2.39Å resolution

Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor

Released: 12 Nov 2014

DOI: 10.2210/pdb4tot/pdb

Source organisms:

Primary publication:
Potent nonimmunosuppressive cyclophilin inhibitors with improved pharmaceutical properties and decreased transporter inhibition.

Fu J, Tjandra M, Becker C, Bednarczyk D, Capparelli M, Elling R, Hanna I, Fujimoto R, Furegati M, Karur S, Kasprzyk T, Knapp M, Leung K, Li X, Lu P, Mergo W, Miault C, Ng S, Parker D, Peng Y, Roggo S, Rivkin A, Simmons RL, Wang M, Wiedmann B, Weiss AH, Xiao L, Xie L, Xu W, Yifru A, Yang S, Zhou B, Sweeney ZK

J Med Chem 57 8503-16 (2014)

PMID: 25310383

Function and Biology Details

Reaction catalysed:

Peptidylproline (omega=180) = peptidylproline (omega=0)

Biochemical function:

peptidyl-prolyl cis-trans isomerase activity

Biological process:

protein folding

Cellular component:

not assigned

Sequence domains:

Structure analysis Details

Assembly composition:

hetero dimer (preferred)

Assembly name:

Peptidyl-prolyl cis-trans isomerase F, mitochondrial and peptide (preferred)

PDBe Complex ID:

PDB-CPX-151355 (preferred)

Entry contents:

2 distinct polypeptide molecules

Macromolecules (2 distinct):

Peptidyl-prolyl cis-trans isomerase F, mitochondrial Chains: A, B, C, D

Molecule details ›

Chains: A, B, C, D
Length: 165 amino acids
Theoretical weight: 17.69 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:

Canonical: P29117 (Residues: 43-206; Coverage: 80%)

Gene name: Ppif
Sequence domains: Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD
Structure domains: Cyclophilin-like

nonimmunosuppressive inhibitor Chains: E, F, G, H

Molecule details ›

Chains: E, F, G, H
Length: 11 amino acids
Theoretical weight: 1.36 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:

7 modified residues:

Experiments and Validation Details

Entry percentile scores

X-ray source: RIGAKU FR-E+ SUPERBRIGHT

Spacegroup: P1

Unit cell:

a: 50.197Å b: 57.286Å c: 75.274Å

α: 89.95° β: 83.81° γ: 89.86°

R-values:

R R_work R_free

0.198 0.196 0.23

Expression systems:

Escherichia coli
Not provided

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Assembly 1 (mmCIF; gz)
Assembly 2 (mmCIF; gz)
Assembly 3 (mmCIF; gz)
Assembly 4 (mmCIF; gz)
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Citations

5 review citations

Current therapy for chronic hepatitis C: The role of direct-acting antivirals.

Li et al. (2017)

4 more

1 mention without citation

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease.

Liao et al. (2016)