4ZOJ

Methylsulfanyl-containing inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Inhibitor bound in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD).

Evans, G.L.Baker, E.N.Lott, J.S.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anthranilate phosphoribosyltransferase
A, B
379Mycobacterium tuberculosis H37RaMutation(s): 0 
Gene Names: trpDMRA_2208
EC: 2.4.2.18
UniProt
Find proteins for A5U4M0 (Mycobacterium tuberculosis (strain ATCC 25177 / H37Ra))
Explore A5U4M0 
Go to UniProtKB:  A5U4M0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA5U4M0
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PRP
Query on PRP

Download Ideal Coordinates CCD File 
E [auth A],
J [auth B]
1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose
C5 H13 O14 P3
PQGCEDQWHSBAJP-TXICZTDVSA-N
61L
Query on 61L

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
4-methyl-2-{[2-methyl-6-(methylsulfanyl)phenyl]amino}benzoic acid
C16 H17 N O2 S
WXFNVVGSUPMXIF-UHFFFAOYSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
IMD
Query on IMD

Download Ideal Coordinates CCD File 
L [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
H [auth B],
I [auth B]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.2α = 90
b = 111.2β = 90
c = 78.5γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
REFMACrefinement
Blu-Icedata collection

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biopharma TRI fundNew Zealand76673
Health Research Council (HRC)New Zealand12/110C

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-11
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.2: 2019-07-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary