8CCJ

Crystal structure of Mycobacterium smegmatis thioredoxin reductase in complex with NADPH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

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

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thioredoxin reductase319Mycolicibacterium smegmatis MC2 155Mutation(s): 0 
Gene Names: trxB
UniProt
Find proteins for A0R7I9 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155))
Explore A0R7I9 
Go to UniProtKB:  A0R7I9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0R7I9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
FAD
Query on FAD

Download Ideal Coordinates CCD File 
B [auth A]FLAVIN-ADENINE DINUCLEOTIDE
C27 H33 N9 O15 P2
VWWQXMAJTJZDQX-UYBVJOGSSA-N
NAP (Subject of Investigation/LOI)
Query on NAP

Download Ideal Coordinates CCD File 
C [auth A]NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS
Query on DMS

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A],
H [auth A]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
J [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.180 
  • R-Value Observed: 0.181 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.92α = 90
b = 67.92β = 90
c = 154.99γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentGermanyTTU 02.906

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-07
    Type: Initial release