4KPR

Tetrameric form of rat selenoprotein thioredoxin reductase 1

• PDB DOI: https://doi.org/10.2210/pdb4KPR/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-05-14 Released: 2014-05-14 
• Deposition Author(s): Lindqvist, Y., Sandalova, T., Xu, J., Arner, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.187 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 

Starting Model: experimental

Literature

The Trp114 residue of thioredoxin reductase 1 is an electron relay sensor for oxidative stress

Xu, J., Eriksson, S.E., Cebula, M., Sandalova, T., Hedstrom, E., Pader, I., Cheng, Q., Myers, C.R., Nagy, P., Hellman, U., Selivanova, G., Lindqvist, Y., J Arner, E.S.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 223.52 kDa 
• Atom Count: 15,853 
• Modelled Residue Count: 1,937 
• Deposited Residue Count: 1,996 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase 1, cytoplasmic	A [auth E], B [auth F], C [auth A], D [auth B]	499	Rattus norvegicus	Mutation(s): 0  Gene Names: Trxr1, Txnrd1, Txnrd1 Trxr1 EC: 1.8.1.9 (PDB Primary Data), 1.11.1.2 (UniProt)
UniProt
Find proteins for O89049 (Rattus norvegicus) Explore O89049  Go to UniProtKB:  O89049

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	I [auth E], N [auth F], R [auth A], T [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
MPD	F [auth E], G [auth E], H [auth E], L [auth F], M [auth F], O [auth A], P [auth A], Q [auth A], S [auth B]	(4S)-2-METHYL-2,4-PENTANEDIOL C6 H14 O2 SVTBMSDMJJWYQN-YFKPBYRVSA-N
SO3	E, J [auth F], K [auth F]	SULFITE ION O3 S LSNNMFCWUKXFEE-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SE7	A [auth E], B [auth F], C [auth A], D [auth B]	L-PEPTIDE LINKING	C3 H7 N O4 Se		SEC

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.187 
• R-Value Work: 0.160 
• R-Value Observed: 0.162 
• Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.99	α = 90
b = 162.99	β = 90
c = 236.44	γ = 120

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-05-14 
Deposition Author(s): Lindqvist, Y., Sandalova, T., Xu, J., Arner, E.

Revision History  

• Version 1.0: 2014-05-14
  Type: Initial release
  
• Version 1.1: 2014-08-20
  Changes: Structure summary
• Version 2.0: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Polymer sequence, Refinement description