6GS6 | pdb_00006gs6

Cyclophilin A single mutant D66A in complex with an inhibitor.

PDB DOI: https://doi.org/10.2210/pdb6GS6/pdb

Classification: ISOMERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2018-06-13 Released: 2019-06-26
Deposition Author(s): Georgiou, C., De Simone, A., Juarez-Jimenez, J., Walkinshaw, M.D., Michel, J.
Funding Organization(s): European Research Council

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free:
0.170 (Depositor), 0.176 (DCC)
R-Value Work:
0.150 (Depositor), 0.155 (DCC)
R-Value Observed:
0.151 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Dynamic design: manipulation of millisecond timescale motions on the energy landscape of cyclophilin A

Juarez-Jimenez, J., Gupta, A.A., Karunanithy, G., May, A., Georgiou, C., Ioannidis, H., De Simone, A., Barlow, P.N., Hulme, A.N., Walkinshaw, M.D., Baldwin, A., Michel, J.

(2020) Chem Sci

DOI: https://doi.org/10.1039/C9SC04696H

Macromolecule Content

Total Structure Weight: 18.32 kDa
Atom Count: 1,505
Modeled Residue Count: 160
Deposited Residue Count: 165
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EA4 Query on EA4 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ethyl N-[(4-aminobenzyl)carbamoyl]glycinate C₁₂ H₁₇ N₃ O₃ UCMPTJMHPJQEED-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
DMS Query on DMS Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
EA4	BindingDB: 6GS6	Ki: 1.68e+4 (nM) from 1 assay(s)
EA4	BindingDB: 6GS6	IC50: 1.31e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.16 Å
R-Value Free: 0.170 (Depositor), 0.176 (DCC)
R-Value Work: 0.150 (Depositor), 0.155 (DCC)
R-Value Observed: 0.151 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.01	α = 90
b = 63.01	β = 90
c = 94.72	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
pointless	data scaling
REFMAC	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-06-26

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council	United Kingdom	No. 336289

Revision History (Full details and data files)

Version 1.0: 2019-06-26
Type: Initial release
Version 1.1: 2020-07-08
Changes: Database references
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description