5DDL

Crystal Structure of WT Human Glutathione Transferase Pi soaked with a metalloid then back-soaked with glutathione

PDB DOI: https://doi.org/10.2210/pdb5DDL/pdb

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

Deposited: 2015-08-25 Released: 2016-10-26
Deposition Author(s): Parker, L.J., Parker, M.W., Morton, C.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.178
R-Value Work: 0.138
R-Value Observed: 0.140

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-based Therapeutics

Parker, L.J., Parker, M.W., Morton, C.J., Bocedi, A., Ascher, D.B., Aitken, J.B., Harris, H.H., Lo Bello, M., Ricci, G.

To be published.

Macromolecule Content

Total Structure Weight: 49.47 kDa
Atom Count: 3,838
Modelled Residue Count: 419
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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
5AU Query on 5AU Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B]	D [auth A], H [auth B]	Di-glutathione-PhenylArsine C₂₆ H₃₇ As N₆ O₁₂ S₂ PIQQHKNUDQAGPN-XSLAGTTESA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain H [auth B]
GSH Query on GSH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B]	E [auth A], I [auth B]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Interactions & Density Focus chain E [auth A] Focus chain I [auth B]
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] mmCIF format, chain C [auth A] mmCIF 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]
SO4 Query on SO4 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]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B]	J [auth B], K [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.98 Å
R-Value Free: 0.178
R-Value Work: 0.138
R-Value Observed: 0.140
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.665	α = 90
b = 89.795	β = 98.08
c = 68.854	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-10-26

Deposition Author(s):

Parker, L.J.

Parker, M.W.

Morton, C.J.

Revision History (Full details and data files)

Version 1.0: 2016-10-26
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description

Prepare Data

Validate Data

Deposit Data

Help and Resources

5DDL

Crystal Structure of WT Human Glutathione Transferase Pi soaked with a metalloid then back-soaked with glutathione

Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-based Therapeutics

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)