1CWO | pdb_00001cwo

HUMAN CYCLOPHILIN A COMPLEXED WITH THR2, LEU5, D-HIV8, LEU10 CYCLOSPORIN

PDB DOI: https://doi.org/10.2210/pdb1CWO/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Homo sapiens, Tolypocladium inflatum
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 1998-06-05 Released: 1998-08-12
Deposition Author(s): Mikol, V., Kallen, J., Taylor, P., Walkinshaw, M.D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Conformational Differences of an Immunosuppressant Peptolide in a Single Crystal and in a Crystal Complex with Human Cyclophilin A.

Mikol, V., Taylor, P., Kallen, J., Walkinshaw, M.D.

(1998) J Mol Biology 283: 451

PubMed: 9769217 Search on PubMed
DOI: https://doi.org/10.1006/jmbi.1998.2109
Primary Citation Related Structures:
1CWO

PubMed Abstract:
The crystal structure of (Thr2, Leu5, d-Hiv8, Leu10)-cyclosporin (cyclic peptolide SDZ 214-103) has been determined as the unbound crystal form and as a complex with human cyclophilin A. This pair of structures provides an example of a significant difference in conformation between free and bound ligand in crystals. The conformation of the unbound form is unlike that of both free and bound conformations of cyclosporin A (with the amide bond between residues 3 and 4 in the cis conformation), while the bound conformation is similar to that of CsA bound to cyclophilin. The cyclophilin-bound conformations of both ligands are similar, though this involves a significantly different waterellipsisligand hydrogen-bonding structure, which compensates for the chemical differences between the two ligands.

Organizational Affiliation

The University of Edinburgh, Michael Swann Building, Edinburgh, EH9 3JR, UK.

Macromolecule Content

Total Structure Weight: 19.3 kDa
Atom Count: 1,570
Modeled Residue Count: 176
Deposited Residue Count: 176
Unique protein chains: 2

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE 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 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
CYCLOSPORIN C	B [auth C]	11	Tolypocladium inflatum	Mutation(s): 3

Small Molecules

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
BMT Query on BMT	B [auth C]	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
MLE Query on MLE	B [auth C]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	B [auth C]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	B [auth C]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY
VAD Query on VAD	B [auth C]	L-PEPTIDE LINKING	C₅ H₁₀ O₃		VAL

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001123 Query on PRD_001123	B [auth C]	Cyclosporin C variant (DAL 1 to VAD, MLE 3 to LEU, VAL 9 to LEU)	Cyclic peptide / Immunosuppressant		Interactions Focus chain B [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.86 Å

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.41	α = 90
b = 57.44	β = 90
c = 71.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
XENGEN	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 1998-08-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1998-08-12
Type: Initial release
Version 1.1: 2011-06-14
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2011-07-27
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary
Version 1.4: 2012-12-12
Changes: Other
Version 1.5: 2013-06-26
Changes: Other
Version 1.6: 2018-04-18
Changes: Data collection, Other
Version 1.7: 2023-08-09
Changes: Database references, Derived calculations, Refinement description