7PCJ | pdb_00007pcj

X-ray structure of CypA-C52AK125C/CsA/aromatic foldamer complex

PDB DOI: https://doi.org/10.2210/pdb7PCJ/pdb

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens, Tolypocladium inflatum, synthetic construct
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2021-08-03 Released: 2022-07-13
Deposition Author(s): Vallade, M., Langlois d'Estaintot, B., Fischer, L., Buratto, J., Savko, M., Huc, I.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.219 (Depositor), 0.242 (DCC)
R-Value Work:
0.177 (Depositor)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Literature

X-ray structure of a cystein mutant of Cyclophilin A tethered to an aromatic oligoamide foldamer complexed with Cyclosporin A

Fischer, L., Savko, M., Langlois d'Estaintot, B., Buratto, J., Vallade, M., Huc, I.

To be published.

Macromolecule Content

Total Structure Weight: 41.45 kDa
Atom Count: 3,009
Modeled Residue Count: 364
Deposited Residue Count: 366
Unique protein chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A, C [auth D]	165	Homo sapiens	Mutation(s): 1 Gene Names: PPIA, CYPA 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 A	B, D [auth E]	11	Tolypocladium inflatum	Mutation(s): 0

Find similar proteins by: Sequence | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Aromatic foldamer	E [auth F], F [auth C]	7	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	B, D [auth E]	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	B, D [auth E]	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	B, D [auth E]	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	B, D [auth E]	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	B, D [auth E]	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	B, D [auth E]	PEPTIDE LINKING	C₃ H₇ N O₂		GLY
QUJ Query on QUJ	E [auth F], F [auth C]	L-PEPTIDE LINKING	C₁₄ H₁₆ N₂ O₃		--
QUK Query on QUK	E [auth F], F [auth C]	L-PEPTIDE LINKING	C₁₃ H₁₅ N₃ O₃		--
QVS Query on QVS	E [auth F], F [auth C]	L-PEPTIDE LINKING	C₁₀ H₈ N₂ O₃		--

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	B, D [auth E]	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain B Focus chain D [auth E] Interactions & Density Focus chain B Focus chain D [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.219 (Depositor), 0.242 (DCC)
R-Value Work: 0.177 (Depositor)
R-Value Observed: 0.179 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.474	α = 90
b = 70.891	β = 102.7
c = 64.09	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-13

Deposition Author(s):

Vallade, M.

Langlois d'Estaintot, B.

Funding Organization	Location	Grant Number
Other government	France	--

Revision History (Full details and data files)

Version 1.0: 2022-07-13
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Derived calculations, Refinement description
Version 2.0: 2024-09-04
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Polymer sequence, Source and taxonomy, Structure summary
Version 3.0: 2024-10-02
Changes: Atomic model, Data collection, Derived calculations
Version 3.1: 2024-11-13
Changes: Structure summary