2GS3

Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)

PDB DOI: https://doi.org/10.2210/pdb2GS3/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2006-04-25 Released: 2006-05-09
Deposition Author(s): Johansson, C., Kavanagh, K.L., Rojkova, A., Gileadi, O., von Delft, F., Arrowsmith, C., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free:
0.191 (Depositor), 0.200 (DCC)
R-Value Work:
0.172 (Depositor), 0.180 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 4(GPX4)

Johansson, C., Kavanagh, K.L., Rojkova, A., Gileadi, O., von Delft, F., Arrowsmith, C., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

To be published.

Macromolecule Content

Total Structure Weight: 21.22 kDa
Atom Count: 1,500
Modelled Residue Count: 171
Deposited Residue Count: 185
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholipid hydroperoxide glutathione peroxidase	A	185	Homo sapiens	Mutation(s): 1 Gene Names: GPX4 EC: 1.11.1.12 (PDB Primary Data), 1.11.1.9 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens) Explore P36969 Go to UniProtKB: P36969
PHAROS: P36969 GTEx: ENSG00000167468
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P36969
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.191 (Depositor), 0.200 (DCC)
R-Value Work: 0.172 (Depositor), 0.180 (DCC)
R-Value Observed: 0.173 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.945	α = 90
b = 62.945	β = 90
c = 195.984	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2006-05-09

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2006-05-09
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.3: 2018-01-31
Changes: Database references, Structure summary
Version 1.4: 2021-10-20
Changes: Database references, Derived calculations
Version 1.5: 2023-08-30
Changes: Data collection, Refinement description

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.