3DGH | pdb_00003dgh

Crystal Structure of Drosophila Thioredoxin Reductase, C-terminal 8-residue truncation

PDB DOI: https://doi.org/10.2210/pdb3DGH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2008-06-13 Released: 2009-06-16
Deposition Author(s): Eckenroth, B.E., Hondal, R.J., Everse, S.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free:
0.224 (Depositor), 0.243 (DCC)
R-Value Work:
0.200 (Depositor), 0.223 (DCC)
R-Value Observed:
0.203 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

Crystal Structure of Drosophila Thioredoxin Reductase, C-terminal 8-residue truncation

Eckenroth, B.E., Hondal, R.J., Everse, S.J.

To be published.

Macromolecule Content

Total Structure Weight: 107.03 kDa
Atom Count: 8,058
Modeled Residue Count: 950
Deposited Residue Count: 966
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase 1, mitochondrial	A, B	483	Drosophila melanogaster	Mutation(s): 2 Gene Names: Trxr-1, GR, CG2151 EC: 1.8.1.9
UniProt
Find proteins for P91938 (Drosophila melanogaster) Explore P91938 Go to UniProtKB: P91938
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P91938
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD Query on FAD Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain C [auth A] MOL2 format, chain F [auth B] MOL2 format, chain C [auth A] mmCIF format, chain F [auth B] mmCIF format, chain C [auth A]	C [auth A], F [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain C [auth A] Focus chain F [auth B] Interactions & Density Focus chain C [auth A] Focus chain F [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain H [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain G [auth B] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain G [auth B] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A], E [auth A], G [auth B], H [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth B] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.224 (Depositor), 0.243 (DCC)
R-Value Work: 0.200 (Depositor), 0.223 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.755	α = 90
b = 135.755	β = 90
c = 132.527	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Locally	data collection

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2009-06-16

Deposition Author(s):

Eckenroth, B.E.

Revision History (Full details and data files)

Version 1.0: 2009-06-16
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: 2024-10-30
Changes: Data collection, Structure summary

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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.