7DDV

Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor

• PDB DOI: https://doi.org/10.2210/pdb7DDV/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Mycolicibacterium smegmatis
• Mutation(s): No 


• Deposited: 2020-10-29 Released: 2021-11-10 
• Deposition Author(s): Tiwari, S., Pal, R.K., Biswal, B.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 

Literature

Crystal structure of M.tuberculosis imidazole glycerol phosphate dehydratase in complex with an inhibitor

Tiwari, S., Pal, R.K., Biswal, B.K.

To be published.

Biological Assembly 1  

Global Symmetry: Octahedral - O  (Explore in 3D)
Global Stoichiometry: Homo 24-mer - A24 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 24.03 kDa 
• Atom Count: 1,611 
• Modelled Residue Count: 190 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Imidazoleglycerol-phosphate dehydratase	A	216	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: hisB, Rv1601, MTCY336.03c EC: 4.2.1.19
UniProt
Find proteins for P9WML9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WML9  Go to UniProtKB:  P9WML9

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
H3L (Subject of Investigation/LOI)	D [auth A]	(1S)-1-(2-methyl-1,2,4-triazol-3-yl)ethanamine C5 H10 N4 OCXIKYJPCILJLE-BYPYZUCNSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	B [auth A], C [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.205 
• R-Value Work: 0.156 
• Space Group: P 4 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111.829	α = 90
b = 111.829	β = 90
c = 111.829	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-11-10 
Deposition Author(s): Tiwari, S., Pal, R.K., Biswal, B.K.

Revision History  

• Version 1.0: 2021-11-10
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Derived calculations, Refinement description