5DJM

Structure of WT Human Glutathione Transferase in complex with cisplatin in the absence of glutathione.

PDB DOI: https://doi.org/10.2210/pdb5DJM/pdb

Classification: transferase/transferase inhibitor
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2015-09-02 Released: 2016-11-02
Deposition Author(s): Parker, L.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.207
R-Value Observed: 0.208

wwPDB Validation 3D Report Full Report

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

Literature

A structure-based mechanism of cisplatin resistance mediated by Glutathione Transferase P1-1

Parker, L.J., Italiano, L.C., Hancock, N.C., Aitken, J., Harris, H.H., Hansen, G., Ascher, D.B., Morton, C.J., Parker, M.W., Lo Bello, M.

(2019) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 47.73 kDa
Atom Count: 3,242
Modelled Residue Count: 396
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	210	Homo sapiens	Mutation(s): 0 Gene Names: GSTP1, FAEES3, GST3 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09211
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain F [auth B] MOL2 format, chain C [auth A] MOL2 format, chain F [auth B]	C [auth A], F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
PT Query on PT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B]	D [auth A], E [auth A], G [auth B]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.240
R-Value Work: 0.207
R-Value Observed: 0.208
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.517	α = 90
b = 90.13	β = 97.85
c = 68.943	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-11-02

Deposition Author(s):

Parker, L.J.

Revision History (Full details and data files)

Version 1.0: 2016-11-02
Type: Initial release
Version 1.1: 2017-11-22
Changes: Derived calculations, Refinement description
Version 1.2: 2019-06-19
Changes: Data collection, Database references
Version 1.3: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5DJM

Structure of WT Human Glutathione Transferase in complex with cisplatin in the absence of glutathione.

A structure-based mechanism of cisplatin resistance mediated by Glutathione Transferase P1-1

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)