Biological Assembly 1  

 3D View: Structure

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 18561.07 
• Atom Count: 1296 
• Residue Count: 170 
• Unique protein chains: 2

1VBS

STRUCTURE OF CYCLOPHILIN COMPLEXED WITH (D)ALA CONTAINING TETRAPEPTIDE

• DOI: 10.2210/pdb1VBS/pdb

• Classification: ISOMERASE/ ISOMERASE SUBSTRATE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


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

---

Experimental Data Snapshot

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

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 


• 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.

---

Organizational Affiliation: 

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

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
CYCLOPHILIN A	A	165	Homo sapiens	Mutation(s): 0  Gene 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
Molecule	Chains	Sequence Length	Organism	Details
TETRAPEPTIDE	B	5	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
NIT	B	NON-POLYMER	C6 H6 N2 O2		--
DAL	B	D-PEPTIDE LINKING	C3 H7 N O2		--

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 = 67.100	α = 90.00
b = 67.100	β = 90.00
c = 95.200	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-06-16 
• 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
  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