5BYT

PRPP complexed with a single Mg in the active site of Mycobacterium tuberculosis anthranilate phosphoribosyltransferase (AnPRT; trpD)

• PDB DOI: https://doi.org/10.2210/pdb5BYT/pdb

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


• Deposited: 2015-06-11 Released: 2016-07-20 
• 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: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 

Starting Model: experimental

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)

Macromolecule Content

• Total Structure Weight: 78.72 kDa 
• Atom Count: 5,455 
• Modelled Residue Count: 686 
• Deposited Residue Count: 758 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anthranilate phosphoribosyltransferase	A, B	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
PRP	D [auth A], F [auth B]	1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose C5 H13 O14 P3 PQGCEDQWHSBAJP-TXICZTDVSA-N
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.271 
• R-Value Work: 0.223 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.011	α = 90
b = 81.192	β = 90
c = 78.578	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-07-20 
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: 2016-07-20
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Data collection, Derived calculations
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary