3PMP | pdb_00003pmp

Crystal Structure of Cyclophilin A from Moniliophthora perniciosa in complex with Cyclosporin A

PDB DOI: https://doi.org/10.2210/pdb3PMP/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Moniliophthora perniciosa, Tolypocladium inflatum
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-11-17 Released: 2011-11-23
Deposition Author(s): Monzani, P., Pereira, H.M., Gramacho, K.P., Meirelles, F.V., Oliva, G., Cascardo, J.C.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free:
0.189 (Depositor), 0.190 (DCC)
R-Value Work:
0.164 (Depositor), 0.160 (DCC)
R-Value Observed:
0.165 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Cyclophilin A from Moniliophthora perniciosa

Monzani, P., Pereira, H.M., Gramacho, K.P., Meirelles, F.V., Oliva, G., Cascardo, J.C.C.

To be published.

Macromolecule Content

Total Structure Weight: 38.12 kDa
Atom Count: 3,079
Modeled Residue Count: 348
Deposited Residue Count: 350
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cyclophilin A	A, B	164	Moniliophthora perniciosa	Mutation(s): 0 Gene Names: Cpy EC: 5.2.1.8
UniProt
Find proteins for E3P6K5 (Moniliophthora perniciosa) Explore E3P6K5 Go to UniProtKB: E3P6K5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	E3P6K5
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, D	11	Tolypocladium inflatum	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	C, D	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	C, D	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
MLE Query on MLE	C, D	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	C, D	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	C, D	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, D	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain C Focus chain D Interactions & Density Focus chain C Focus chain D

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.47 Å
R-Value Free: 0.189 (Depositor), 0.190 (DCC)
R-Value Work: 0.164 (Depositor), 0.160 (DCC)
R-Value Observed: 0.165 (Depositor)

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.028	α = 90
b = 104.028	β = 90
c = 61.305	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
MOLREP	phasing
PHENIX	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-23

Deposition Author(s):

Meirelles, F.V.

Cascardo, J.C.C.

Revision History (Full details and data files)

Version 1.0: 2011-11-23
Type: Initial release
Version 1.1: 2013-02-27
Changes: Other
Version 1.2: 2015-01-28
Changes: Other
Version 1.3: 2023-05-31
Changes: Database references, Derived calculations

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.