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.

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
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wwPDB Validation 3D Report Full Report

Validation slider image for 1VBT

This is version 1.4 of the entry. See complete history.

Literature

Insight Into Conversion of Substrate to Inhibitor

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

To be published.

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

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on 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

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Entry History

Deposition Data

Released Date: 1999-01-13

Deposition Author(s):

Schutkowski, M.

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.