3N9J | pdb_00003n9j

Structure of human Glutathione Transferase Pi class in complex with Ethacraplatin

PDB DOI: https://doi.org/10.2210/pdb3N9J/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2010-05-30 Released: 2011-05-11
Deposition Author(s): Parker, L.J., Parker, M.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.218 (Depositor), 0.218 (DCC)
R-Value Work:
0.178 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (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

Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation.

Parker, L.J., Italiano, L.C., Morton, C.J., Hancock, N.C., Ascher, D.B., Aitken, J.B., Harris, H.H., Campomanes, P., Rothlisberger, U., De Luca, A., Lo Bello, M., Ang, W.H., Dyson, P.J., Parker, M.W.

To be published.

Macromolecule Content

Total Structure Weight: 48.1 kDa
Atom Count: 3,739
Modeled Residue Count: 416
Deposited Residue Count: 420
Unique protein chains: 1

Macromolecules

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| 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: 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EAA Query on EAA Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain K [auth B] MOL2 format, chain E [auth A] MOL2 format, chain K [auth B] mmCIF format, chain E [auth A] mmCIF format, chain K [auth B]	E [auth A], K [auth B]	ETHACRYNIC ACID C₁₃ H₁₂ Cl₂ O₄ AVOLMBLBETYQHX-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain K [auth B] Interactions & Density Focus chain E [auth A] Focus chain K [auth B]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B]	D [auth A], I [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain I [auth B]
PT Query on PT 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]	PLATINUM (II) ION Pt HRGDZIGMBDGFTC-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B]	F [auth A], H [auth B], J [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
EAA	BindingDB: 3N9J	IC50: min: 3400, max: 2.60e+4 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.218 (Depositor), 0.218 (DCC)
R-Value Work: 0.178 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.806	α = 90
b = 89.994	β = 98.24
c = 68.87	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: 2011-05-11

Deposition Author(s):

Parker, L.J.

Parker, M.W.

Revision History (Full details and data files)

Version 1.0: 2011-05-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

3N9J | pdb_00003n9j

Structure of human Glutathione Transferase Pi class in complex with Ethacraplatin

Literature

Studies of glutathione transferase P1-1 bound to a platinum(IV)-based anticancer compound reveal the molecular basis of its activation.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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