3KMO | pdb_00003kmo

Crystal Structure of the Human GST Pi C47S/Y108V Double Mutant in Complex with the Ethacrynic Acid-Glutathione Conjugate (Grown in the Absence of the Reducing Agent DTT)

PDB DOI: https://doi.org/10.2210/pdb3KMO/pdb

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

Deposited: 2009-11-11 Released: 2010-03-23
Deposition Author(s): Parker, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.254 (Depositor), 0.254 (DCC)
R-Value Work:
0.165 (Depositor), 0.168 (DCC)
R-Value Observed:
0.169 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Diuretic drug binding to human glutathione transferase P1-1: potential role of CYS101 revealed in the double mutant C47S/Y108V

Quesada-Soriano, I., Parker, L.J., Primavera, A., Wielens, J., Holien, J.K., Casas-Solvas, J.M., Vargas-Berenguel, A., Aguilera, A., Nuccetelli, N., Mazzetti, A.P., Lo Bello, M., Parker, M.W., Garcia-Fuentes, L.

To be published.

Macromolecule Content

Total Structure Weight: 47.79 kDa
Atom Count: 3,566
Modeled Residue Count: 417
Deposited Residue Count: 418
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	209	Homo sapiens	Mutation(s): 2 Gene Names: FAEES3, GST3, GSTP1 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens) Explore P09211 Go to UniProtKB: P09211
PHAROS: P09211 GTEx: ENSG00000084207
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P09211
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain I [auth B] MOL2 format, chain C [auth A] MOL2 format, chain I [auth B] mmCIF format, chain C [auth A] mmCIF format, chain I [auth B]	C [auth A], I [auth B]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]
EAA Query on EAA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth B] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B]	G [auth A], L [auth B]	ETHACRYNIC ACID C₁₃ H₁₂ Cl₂ O₄ AVOLMBLBETYQHX-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Interactions & Density Focus chain G [auth A] Focus chain L [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	D [auth A] E [auth A] F [auth A] H [auth A] J [auth B] D [auth A], E [auth A], F [auth A], H [auth A], J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth A] Focus chain J [auth B] Focus chain K [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
EAA	BindingDB: 3KMO	IC50: min: 3400, max: 2.60e+4 (nM) from 3 assay(s)

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	C [auth A], I [auth B]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain C [auth A] Focus chain I [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.254 (Depositor), 0.254 (DCC)
R-Value Work: 0.165 (Depositor), 0.168 (DCC)
R-Value Observed: 0.169 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.902	α = 90
b = 89.348	β = 90.07
c = 69.383	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
MOSFLM	data reduction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2010-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2011-12-07
Changes: Advisory, Non-polymer description
Version 1.3: 2021-11-10
Changes: Database references, Derived calculations
Version 1.4: 2024-05-29
Changes: Data collection

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.