4KPR | pdb_00004kpr

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.40 Å
R-Value Free:
0.187 (Depositor), 0.192 (DCC)
R-Value Work:
0.160 (Depositor), 0.170 (DCC)
R-Value Observed:
0.162 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O89049
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain I [auth E] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain N [auth F] MOL2 format, chain I [auth E] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain N [auth F] mmCIF format, chain I [auth E] mmCIF format, chain R [auth A] mmCIF format, chain T [auth B] mmCIF format, chain N [auth F]	I [auth E], N [auth F], R [auth A], T [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain I [auth E] Focus chain N [auth F] Focus chain R [auth A] Focus chain T [auth B] Interactions & Density Focus chain I [auth E] Focus chain N [auth F] Focus chain R [auth A] Focus chain T [auth B]
MPD Query on MPD Download:Ideal Coordinates CCD File SDF format, chain G [auth E] SDF format, chain H [auth E] SDF format, chain L [auth F] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain Q [auth A] SDF format, chain M [auth F] SDF format, chain F [auth E] MOL2 format, chain G [auth E] MOL2 format, chain H [auth E] MOL2 format, chain L [auth F] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain M [auth F] MOL2 format, chain F [auth E] mmCIF format, chain G [auth E] mmCIF format, chain H [auth E] mmCIF format, chain L [auth F] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain S [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain M [auth F] mmCIF format, chain F [auth E]	F [auth E] G [auth E] H [auth E] L [auth F] M [auth F] 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		Interactions Focus chain F [auth E] Focus chain G [auth E] Focus chain H [auth E] Focus chain L [auth F] Focus chain M [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B] Interactions & Density Focus chain F [auth E] Focus chain G [auth E] Focus chain H [auth E] Focus chain L [auth F] Focus chain M [auth F] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain S [auth B]
SO3 Query on SO3 Download:Ideal Coordinates CCD File SDF format, chain J [auth F] SDF format, chain K [auth F] SDF format, chain E MOL2 format, chain J [auth F] MOL2 format, chain K [auth F] MOL2 format, chain E mmCIF format, chain J [auth F] mmCIF format, chain K [auth F] mmCIF format, chain E	E, J [auth F], K [auth F]	SULFITE ION O₃ S LSNNMFCWUKXFEE-UHFFFAOYSA-L		Interactions Focus chain E Focus chain J [auth F] Focus chain K [auth F] Interactions & Density Focus chain E Focus chain J [auth F] Focus chain K [auth F]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SE7 Query on 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 (Depositor), 0.192 (DCC)
R-Value Work: 0.160 (Depositor), 0.170 (DCC)
R-Value Observed: 0.162 (Depositor)

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

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-05-14

Deposition Author(s):

Revision History (Full details and data files)

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