Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 17903.41 
• Atom Count: 1263 
• Residue Count: 164 
• Unique protein chains: 1

4XNC

Crystal structure at room temperature of cyclophilin D in complex with an inhibitor

• DOI: 10.2210/pdb4XNC/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): 1 


• Deposited: 2015-01-15 Released: 2015-08-12 
• Deposition Author(s): Gelin, M., Allemand, F., Labesse, G., Guichou, J.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.186 
• R-Value Work: 0.140 

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.,Sect.D 71: 1777-1787

• PubMed: 26249358 
• DOI: 10.1107/S1399004715010342
• Primary Citation of Related Structures:  
  4ZSD, 4ZSC, 4XRL, 4XRJ, 4XP3, 4XP2, 4XP0, 4XOZ, 4XOY, 4XNE, 4XN6, 4XLD, 3RDC


• 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.

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Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase F, mitochondrial	A	164	Homo sapiens	Mutation(s): 1  Gene Names: PPIF (CYP3) EC: 5.2.1.8
Find proteins for P30405 (Homo sapiens) Go to Gene View: PPIF Go to UniProtKB:  P30405

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
EA4	A	ethyl N-[(4-aminobenzyl)carbamoyl]glycinate C12 H17 N3 O3 UCMPTJMHPJQEED-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.23 Å
• R-Value Free: 0.186 
• R-Value Work: 0.140 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 58.000	α = 90.00
b = 58.000	β = 90.00
c = 88.410	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	phasing
SCALA	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-01-15 
• Released Date: 2015-08-12 
• Deposition Author(s): Gelin, M., Allemand, F., Labesse, G., Guichou, J.F.

Revision History 

• Version 1.0: 2015-08-12
  Type: Initial release
• Version 1.1: 2015-08-19
  Type: Database references