9CUN

Crystal structure of Ami1 from M. tuberculosis in complex with a tetrazole compound

• PDB DOI: https://doi.org/10.2210/pdb9CUN/pdb

• Classification: HYDROLASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2024-07-26 Released: 2024-11-20 
• Deposition Author(s): Martinez-Caballero, S.
• Funding Organization(s): Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

Starting Model: experimental

Literature

Identification of Potential Inhibitors of Mycobacterium tuberculosis Amidases: An Integrated In Silico and Experimental Study

Rosas-Cruz, M., Madariaga Mazon, A., Garcia-Mejia, C.D., Hernandez-Vazquez, E., Gomez-Velasco, H., Jimenez-Faraco, E., Farias-Gaytan, R.S., Hermoso, J.A., Martinez-Caballero, S.

(2024) ACS Omega 

• DOI: https://doi.org/10.1021/acsomega.4c07964

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 23.03 kDa 
• Atom Count: 1,753 
• Modelled Residue Count: 212 
• Deposited Residue Count: 218 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-acetylmuramoyl-L-alanine amidase Rv3717	A	218	Mycobacterium tuberculosis	Mutation(s): 0  Gene Names: Rv3717 EC: 3.5.1.28
UniProt
Find proteins for I6Y4D2 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore I6Y4D2  Go to UniProtKB:  I6Y4D2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1A0I (Subject of Investigation/LOI)	B [auth A]	5-(2-iodophenyl)-2H-tetrazole C7 H5 I N4 BISBCDUUTDMGBR-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 0.200 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: I 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.353	α = 90
b = 103.96	β = 90
c = 130.143	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-11-20 
Deposition Author(s): Martinez-Caballero, S.

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Funding Organization	Location	Grant Number
Programa de Apoyo a Proyectos de Investigacion e Innovacion Tecnologica (PAPIIT)	Mexico	IA205122

Revision History  

• Version 1.0: 2024-11-20
  Type: Initial release