1VBT | pdb_00001vbt

Structure of cyclophilin complexed with sulfur-substituted tetrapeptide AAPF

• PDB DOI: https://doi.org/10.2210/pdb1VBT/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: 2.30 Å
• R-Value Free: 
  0.246 (Depositor) 
• R-Value Work: 
  0.198 (Depositor) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Insight Into Conversion of Substrate to Inhibitor

Zhao, Y., Chen, Y., Schutkowski, M., Fischer, G., Ke, H.

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: 37.15 kDa 
• Atom Count: 2,660 
• Modeled Residue Count: 338 
• Deposited Residue Count: 340 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOPHILIN A	A, B	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
SULFUR-SUBSTITUTED TETRAPEPTIDE	C, D	5	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALT	C, D	L-PEPTIDE LINKING	C3 H7 N O S		ALA

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.246 (Depositor) 
• R-Value Work:  0.198 (Depositor) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.7	α = 90
b = 109.1	β = 90
c = 118.2	γ = 90

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: 2024-11-13
  Changes: Structure summary