2WFJ | pdb_00002wfj

Atomic resolution crystal structure of the PPIase domain of human cyclophilin G in complex with cyclosporin A.

PDB DOI: https://doi.org/10.2210/pdb2WFJ/pdb

Classification: ISOMERASE/IMMUNOSUPPRESSANT
Organism(s): Homo sapiens, Tolypocladium inflatum
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-04-06 Released: 2009-06-16
Deposition Author(s): Stegmann, C.M., Sheldrick, G.M., Wahl, M.C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 0.75 Å
R-Value Free:
0.129 (Depositor), 0.128 (DCC)
R-Value Work:
0.125 (DCC)
R-Value Observed:
0.111 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

The Thermodynamic Influence of Trapped Water Molecules on a Protein-Ligand Interaction.

Stegmann, C.M., Seeliger, D., Sheldrick, G.M., De Groot, B.L., Wahl, M.C.

(2009) Angew Chem Int Ed Engl 48: 5207

PubMed: 19499554 Search on PubMed
DOI: https://doi.org/10.1002/anie.200900481
Primary Citation Related Structures:
2WFI, 2WFJ

PubMed Abstract:
Water molecules doing time: Atomic-resolution crystal structures of the PPIase domain of cyclophilin G, alone and in complex with cyclosporin A, and together with MD simulations and calorimetry, reveal how trapped water molecules influence the thermodynamic profile of a protein-ligand interaction.

Organizational Affiliation

Research Group X-ray Crystallography, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 21.21 kDa
Atom Count: 1,834
Modeled Residue Count: 183
Deposited Residue Count: 190
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE G	A	179	Homo sapiens	Mutation(s): 0 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13427 (Homo sapiens) Explore Q13427 Go to UniProtKB: Q13427
PHAROS: Q13427 GTEx: ENSG00000138398
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13427
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	11	Tolypocladium inflatum	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]

Modified Residues 5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ABA Query on ABA	B	L-PEPTIDE LINKING	C₄ H₉ N O₂		ALA
BMT Query on BMT	B	L-PEPTIDE LINKING	C₁₀ H₁₉ N O₃		THR
DAL Query on DAL	B	D-PEPTIDE LINKING	C₃ H₇ N O₂		--
MLE Query on MLE	B	L-PEPTIDE LINKING	C₇ H₁₅ N O₂		LEU
MVA Query on MVA	B	L-PEPTIDE LINKING	C₆ H₁₃ N O₂		VAL
SAR Query on SAR	B	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	B	Cyclosporin A	Cyclic peptide / Immunosuppressant		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 0.75 Å
R-Value Free: 0.129 (Depositor), 0.128 (DCC)
R-Value Work: 0.125 (DCC)
R-Value Observed: 0.111 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.319	α = 90
b = 64.913	β = 90
c = 69.285	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
XDS	data reduction
XDS	data scaling
SHELX	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Stegmann, C.M.

Sheldrick, G.M.

Wahl, M.C.

Revision History (Full details and data files)

Version 1.0: 2009-06-16
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
Version 1.2: 2011-11-23
Changes: Database references
Version 1.3: 2012-11-30
Changes: Other
Version 1.4: 2019-05-22
Changes: Data collection, Derived calculations, Other, Refinement description
Version 1.5: 2025-04-09
Changes: Data collection, Database references, Derived calculations, Other, Structure summary