8CCK | pdb_00008cck

Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with fragment F2X-Entry H07

• PDB DOI: https://doi.org/10.2210/pdb8CCK/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycolicibacterium smegmatis MC2 155
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2023-01-27 Released: 2024-02-07 
• Deposition Author(s): Fuesser, F.T., Koch, O., Kuemmel, D.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 
  0.242 (Depositor), 0.217 (DCC) 
• R-Value Work: 
  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Fragment-based design of mycobacterial thioredoxin reductase inhibitors based on computational exploration of a huge virtual space

Fuesser, F.T., Otten, P., Junker, A., Kuemmel, D., Koch, O.

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 Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 35.7 kDa 
• Atom Count: 2,603 
• Modeled Residue Count: 305 
• Deposited Residue Count: 319 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thioredoxin reductase	A	319	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0  Gene Names: trxB EC: 1.8.1.9
UniProt
Find proteins for A0R7I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R7I9  Go to UniProtKB:  A0R7I9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FAD	B [auth A]	FLAVIN-ADENINE DINUCLEOTIDE C27 H33 N9 O15 P2 VWWQXMAJTJZDQX-UYBVJOGSSA-N
U8X (Subject of Investigation/LOI)	D [auth A]	~{N}-(4-hydroxyphenyl)-2-pyrazol-1-yl-ethanamide C11 H11 N3 O2 BSUVSWPKCMWXTE-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free:  0.242 (Depositor), 0.217 (DCC) 
• R-Value Work:  0.214 (Depositor), 0.216 (DCC) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.02	α = 90
b = 68.02	β = 90
c = 155.22	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-02-07 
Deposition Author(s): Fuesser, F.T., Koch, O., Kuemmel, D.

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Funding Organization	Location	Grant Number
Other government	Germany	TTU 02.906

Revision History  

• Version 1.0: 2024-02-07
  Type: Initial release
  
• Version 1.1: 2024-11-13
  Changes: Structure summary