4POM | pdb_00004pom

Crystal structures of thioredoxin with mesna at 1.85A resolution

PDB DOI: https://doi.org/10.2210/pdb4POM/pdb

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

Deposited: 2014-02-26 Released: 2014-10-29
Deposition Author(s): Sridhar, V., Chie-Leon, B., Badger, J., Nienaber, V.L., Hausheer, F.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.213 (Depositor), 0.211 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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This is version 1.3 of the entry. See complete history.

Literature

BNP7787 Forms Novel Covalent Adducts on Human Thioredoxin and Modulates Thioredoxin Activity

Parker, A.R., Nienaber, V.L., Petluru, P.N., Sridhar, V., Leverett, B.D., Ayala, P.Y., Zhao, M., Chie-Leon, B., Jair, K., Kochat, H., Badger, J., Hausheer, F.H.

(2014) J Pharmacol Clin Toxicol 2: 1026

Macromolecule Content

Total Structure Weight: 48.49 kDa
Atom Count: 3,520
Modeled Residue Count: 428
Deposited Residue Count: 436
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin	A, B, C, D	109	Homo sapiens	Mutation(s): 4 Gene Names: TXN, TRDX, TRX, TRX1
UniProt & NIH Common Fund Data Resources
Find proteins for P10599 (Homo sapiens) Explore P10599 Go to UniProtKB: P10599
PHAROS: P10599 GTEx: ENSG00000136810
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P10599
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
COM Query on COM Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B]	1-THIOETHANESULFONIC ACID C₂ H₆ O₃ S₂ ZNEWHQLOPFWXOF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.85 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.213 (Depositor), 0.211 (DCC)
R-Value Observed: 0.215 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.536	α = 90
b = 91.776	β = 105.36
c = 57.1	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-10-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-10-29
Type: Initial release
Version 1.1: 2015-03-18
Changes: Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.3: 2024-10-16
Changes: 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.