3RDC

Human Cyclophilin D Complexed with an Inhibitor

Structural Biology Knowledgebase: 3RDC SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.205

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3RDC

Classification: ISOMERASE / ISOMERASE INHIBITOR

Total Structure Weight: 18121.79

Macromolecule Entities
Molecule Chains Length Organism Details
Peptidyl-prolyl cis-trans isomerase F, mitochondrial A 166 Homo sapiens EC#: 5.2.1.8 IUBMB
Fragment: UNP residues 43-207
Mutation: K175I
Gene Name(s): PPIF Gene View CYP3

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
EA4
Query on EA4

A ethyl N-[(4-aminobenzyl)carbamoyl]glycinate
C12 H17 N3 O3
UCMPTJMHPJQEED-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.270
  • R-Value Work: 0.205
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 56.44 α = 90.00
b = 56.44 β = 90.00
c = 87.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2011-04-01
  • Released Date: 2012-03-21
  • Deposition author(s): Colliandre, L., Ahmed-Belkacem, H., Bessin, Y., Pawlotsky, J.M., Guichou, J.F.

Revision History

  • 2015-08-12
    Type: Citation | Details: Citation update