5BNE

Bianthranilate-like inhibitor with 6 atom "line" and phosphonate "hook" fishing for hydrogen bond donors in Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

• PDB DOI: https://doi.org/10.2210/pdb5BNE/pdb

• Classification: TRANSFERASE/TRANSFERASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-05-26 Released: 2016-05-25 
• Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)
• Funding Organization(s): Health Research Council (HRC), FRST (Foundation for Research, Science and Technology)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.235 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Binding and mimicking of the phosphate-rich substrate, PRPP.

Evans, G.L., Baker, E.N., Lott, J.S.

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 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 157.34 kDa 
• Atom Count: 9,740 
• Modelled Residue Count: 1,326 
• Deposited Residue Count: 1,516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B, C, D	379	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: trpD, Rv2192c, MTCY190.03c EC: 2.4.2.18
UniProt
Find proteins for P9WFX5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WFX5  Go to UniProtKB:  P9WFX5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7P3	E [auth A], G [auth B], K [auth D]	2-[(2-carboxyphenyl)amino]-5-[(5-phosphonopentyl)oxy]benzoic acid C19 H22 N O8 P HYMLLKWKTLKWNS-UHFFFAOYSA-N
IMD	F [auth A], H [auth B], I [auth B], J [auth C]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.235 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.3	α = 90
b = 78.4	β = 90.7
c = 117.2	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
Blu-Ice	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-05-25 
Deposition Author(s): Evans, G.L., Baker, E.N., Lott, J.S., TB Structural Genomics Consortium (TBSGC)

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Funding Organization	Location	Grant Number
Health Research Council (HRC)	New Zealand	HRC12/1111
FRST (Foundation for Research, Science and Technology)	New Zealand	UOAX1005

Revision History  

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description