2R37 | pdb_00002r37

Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant)

PDB DOI: https://doi.org/10.2210/pdb2R37/pdb

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

Deposited: 2007-08-29 Released: 2007-09-11
Deposition Author(s): Pilka, E.S., Guo, K., Gileadi, O., Rojkowa, A., von Delft, F., Pike, A.C.W., Kavanagh, K.L., Johannson, C., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.183 (Depositor), 0.190 (DCC)
R-Value Work:
0.151 (Depositor), 0.161 (DCC)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2R37

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

Literature

Crystal structure of human glutathione peroxidase 3 (selenocysteine to glycine mutant).

Pilka, E.S., Guo, K., Gileadi, O., Rojkowa, A., von Delft, F., Pike, A.C.W., Kavanagh, K.L., Johannson, C., Sundstrom, M., Arrowsmith, C.H., Weigelt, J., Edwards, A.M., Oppermann, U.

To be published.

Macromolecule Content

Total Structure Weight: 47.22 kDa
Atom Count: 3,462
Modeled Residue Count: 379
Deposited Residue Count: 414
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione peroxidase 3	A, B	207	Homo sapiens	Mutation(s): 1 Gene Names: GPX3, GPXP EC: 1.11.1.9
UniProt & NIH Common Fund Data Resources
Find proteins for P22352 (Homo sapiens) Explore P22352 Go to UniProtKB: P22352
PHAROS: P22352 GTEx: ENSG00000211445
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22352
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.183 (Depositor), 0.190 (DCC)
R-Value Work: 0.151 (Depositor), 0.161 (DCC)
R-Value Observed: 0.153 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.72	α = 90
b = 61.308	β = 90
c = 100.4	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-11

Deposition Author(s):

Arrowsmith, C.H.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-09-11
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2017-10-25
Changes: Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 2023-08-30
Changes: Data collection, Refinement description

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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.