1ZKF

Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA

• PDB DOI: https://doi.org/10.2210/pdb1ZKF/pdb

• Classification: ISOMERASE/ISOMERASE SUBSTRATE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-02 Released: 2006-04-11 
• Deposition Author(s): Eisenmesser, E.Z., Thai, V., Pozharski, E., Kern, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.168 (Depositor) 

Starting Model: experimental

Literature

Mechanistic Insights of Cyclophilin-A from X-Ray Cyrstallographic and Nuclear Magnet Resonance Investigations

Eisenmesser, E.Z., Thai, V., Pozharski, E., Kern, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 37.29 kDa 
• Atom Count: 2,702 
• Modelled Residue Count: 341 
• Deposited Residue Count: 342 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A, B	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937  Go to UniProtKB:  P62937
PHAROS:  P62937 GTEx:  ENSG00000196262

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Suc-ALA-GLY-PRO-PHE-pNA	C, D	6	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.168 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.757	α = 90
b = 108.82	β = 90
c = 118.726	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-04-11 
Deposition Author(s): Eisenmesser, E.Z., Thai, V., Pozharski, E., Kern, D.

Revision History  

• Version 1.0: 2006-04-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description