1VBS | pdb_00001vbs

STRUCTURE OF CYCLOPHILIN COMPLEXED WITH (D)ALA CONTAINING TETRAPEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb1VBS/pdb

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


• Deposited: 1998-06-16 Released: 1999-01-13 
• Deposition Author(s): Zhao, Y., Chen, Y., Schutkowski, M., Fischer, G., Ke, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Mapping the stereospecificity of peptidyl prolyl cis/trans isomerases.

Schiene, C., Reimer, U., Schutkowski, M., Fischer, G.

(1998) FEBS Lett 432: 202-206

• PubMed: 9720925 
• DOI: https://doi.org/10.1016/s0014-5793(98)00871-0
• Primary Citation Related Structures: 
  1VBS


• PubMed Abstract: 
  

  The stereospecificity of peptidyl prolyl cis/trans isomerases (PPIases) was studied using tetrapeptide substrate analogs in which one amino acid residue was replaced by the cognate D-amino acid in various positions of the peptide chain. Reversed stereocenters around proline markedly increased the rate of the spontaneous trans to cis isomerization of the prolyl bond whereas cis to trans isomerizations were less sensitive. PPIases like human cyclophilin18, human FKBP12, Escherichia coli parvulin10 and the PPIase domain of E. coli trigger factor exhibited stereoselectivity demanding at the P1 to P2' position of the substrate chain. The discriminating factor for stereoselectivity was the lack of formation of the Michaelis complexes of the diastereomeric substrates. However, D-alanine at the P1 position preserved considerable affinity to the active site, and largely prevented activation of the catalytic machinery for all PPIases investigated.

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Organizational Affiliation: 
• Max-Planck Society, Research Unit Enzymology of Protein Folding, Halle/Saale, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 18.56 kDa 
• Atom Count: 1,385 
• Modeled Residue Count: 169 
• Deposited Residue Count: 170 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOPHILIN A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: CYCLOPHILIN 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
TETRAPEPTIDE	B	5	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.1	α = 90
b = 67.1	β = 90
c = 95.2	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-01-13 
Deposition Author(s): Zhao, Y., Chen, Y., Schutkowski, M., Fischer, G., Ke, H.

Revision History  

• Version 1.0: 1999-01-13
  Type: Initial release
  
• Version 1.1: 2008-03-24
  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: 2024-04-03
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary