3RDC | pdb_00003rdc

Human Cyclophilin D Complexed with an Inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 
    0.270 (Depositor), 0.275 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Combining 'dry' co-crystallization and in situ diffraction to facilitate ligand screening by X-ray crystallography.

Gelin, M.Delfosse, V.Allemand, F.Hoh, F.Sallaz-Damaz, Y.Pirocchi, M.Bourguet, W.Ferrer, J.L.Labesse, G.Guichou, J.F.

(2015) Acta Crystallogr D Biol Crystallogr 71: 1777-1787

  • DOI: https://doi.org/10.1107/S1399004715010342
  • Primary Citation Related Structures: 
    3RDC, 4XLD, 4XN6, 4XNC, 4XNE, 4XOY, 4XOZ, 4XP0, 4XP2, 4XP3, 4XRJ, 4XRL, 4ZSC, 4ZSD

  • PubMed Abstract: 

    X-ray crystallography is an established technique for ligand screening in fragment-based drug-design projects, but the required manual handling steps - soaking crystals with ligand and the subsequent harvesting - are tedious and limit the throughput of the process. Here, an alternative approach is reported: crystallization plates are pre-coated with potential binders prior to protein crystallization and X-ray diffraction is performed directly 'in situ' (or in-plate). Its performance is demonstrated on distinct and relevant therapeutic targets currently being studied for ligand screening by X-ray crystallography using either a bending-magnet beamline or a rotating-anode generator. The possibility of using DMSO stock solutions of the ligands to be coated opens up a route to screening most chemical libraries.


  • Organizational Affiliation
    • CNRS, UMR5048 - Université de Montpellier, Centre de Biochimie Structurale, 34090 Montpellier, France.

Macromolecule Content 

  • Total Structure Weight: 18.12 kDa 
  • Atom Count: 1,473 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 166 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase F, mitochondrial166Homo sapiensMutation(s): 1 
Gene Names: PPIFCYP3
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens)
Explore P30405 
Go to UniProtKB:  P30405
PHAROS:  P30405
GTEx:  ENSG00000108179 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30405
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EA4

Query on EA4



Download:Ideal Coordinates CCD File
B [auth A]ethyl N-[(4-aminobenzyl)carbamoyl]glycinate
C12 H17 N3 O3
UCMPTJMHPJQEED-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free:  0.270 (Depositor), 0.275 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.208 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.445α = 90
b = 56.445β = 90
c = 86.995γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
X-PLORmodel building
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2015-08-12
    Changes: Database references
  • Version 1.2: 2016-10-19
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description