2F8A | pdb_00002f8a

Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 1

• PDB DOI: https://doi.org/10.2210/pdb2F8A/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-12-02 Released: 2005-12-13 
• Deposition Author(s): Kavanagh, K.L., Johansson, C., Smee, C., Gileadi, O., von Delft, F., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.156 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the selenocysteine to glycine mutant of human glutathione peroxidase 1

Kavanagh, K.L., Johansson, C., Smee, C., Gileadi, O., von Delft, F., Oppermann, U.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 46.5 kDa 
• Atom Count: 3,393 
• Modeled Residue Count: 370 
• Deposited Residue Count: 416 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione peroxidase 1	A, B	208	Homo sapiens	Mutation(s): 0  Gene Names: GPX1 EC: 1.11.1.9 (PDB Primary Data), 1.11.1.12 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P07203 (Homo sapiens) Explore P07203  Go to UniProtKB:  P07203
PHAROS:  P07203 GTEx:  ENSG00000233276

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MLA	C [auth A], D [auth B]	MALONIC ACID C3 H4 O4 OFOBLEOULBTSOW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.156 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.592	α = 90
b = 59.376	β = 119.41
c = 81.132	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-12-13 
Deposition Author(s): Kavanagh, K.L., Johansson, C., Smee, C., Gileadi, O., von Delft, F., Weigelt, J., Sundstrom, M., Edwards, A., Oppermann, U., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2005-12-13
  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: 2015-04-29
  Changes: Non-polymer description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description