1VBS

STRUCTURE OF CYCLOPHILIN COMPLEXED WITH (D)ALA CONTAINING TETRAPEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

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 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 ster ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CYCLOPHILIN A
A
165Homo sapiensGene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TETRAPEPTIDE
B
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
NIT
Query on NIT
B
NON-POLYMERC6 H6 N2 O2

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DAL
Query on DAL
B
D-PEPTIDE LINKINGC3 H7 N O2

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.198 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 67.100α = 90.00
b = 67.100β = 90.00
c = 95.200γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORphasing
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-01-13
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance