2Z6W

Crystal structure of human cyclophilin D in complex with cyclosporin A

PDB DOI: https://doi.org/10.2210/pdb2Z6W/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Homo sapiens, Tolypocladium inflatum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2007-08-09 Released: 2008-04-29
Deposition Author(s): Kajitani, K., Fujihashi, M., Kobayashi, Y., Shimizu, S., Tsujimoto, Y., Miki, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.96 Å
R-Value Free: 0.153
R-Value Work: 0.129
R-Value Observed: 0.130

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

Crystal Structure of Human Cyclophilin D in Complex with its Inhibitor, Cyclosporin a at 0.96-A Resolution.

Kajitani, K., Fujihashi, M., Kobayashi, Y., Shimizu, S., Tsujimoto, Y., Miki, K.

(2008) Proteins 70: 1635

PubMed: 18076075 Search on PubMed
DOI: https://doi.org/10.1002/prot.21855
Primary Citation of Related Structures:
2Z6W

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8502, Japan.

Macromolecule Content

Total Structure Weight: 38.2 kDa
Atom Count: 3,528
Modelled Residue Count: 350
Deposited Residue Count: 352
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE	A, B	165	Homo sapiens	Mutation(s): 1 Gene Names: PPIF, CYP3 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P30405 (Homo sapiens) Explore P30405 Go to UniProtKB: P30405
PHAROS: P30405 GTEx: ENSG00000108179
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P30405
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
CYCLOSPORIN A	C [auth M], D [auth N]	11	Tolypocladium inflatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	C [auth M], D [auth N]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	C [auth M], D [auth N]	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
MLE Query on MLE	C [auth M], D [auth N]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	C [auth M], D [auth N]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	C [auth M], D [auth N]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000142 Query on PRD_000142	C [auth M], D [auth N]	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain C [auth M] Focus chain D [auth N] Interactions & Density Focus chain C [auth M] Focus chain D [auth N]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.96 Å
R-Value Free: 0.153
R-Value Work: 0.129
R-Value Observed: 0.130
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.882	α = 90
b = 69.313	β = 90
c = 112.077	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-04-29
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: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.6: 2023-11-15
Changes: Data collection, Derived calculations