5NRQ | pdb_00005nrq

Mtb TMK crystal structure in complex with compound 33

• PDB DOI: https://doi.org/10.2210/pdb5NRQ/pdb

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


• Deposited: 2017-04-25 Released: 2018-08-08 
• Deposition Author(s): Merceron, R., Song, L., Munier-Lehmann, H., Van Calenbergh, S., Savvides, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Starting Model: experimental

Literature

Mtb TMK crystal structure in complex with compound LS3112

Merceron, R., Song, L., Munier-Lehmann, H., Van Calenbergh, S., Savvides, S.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 46.32 kDa 
• Atom Count: 2,858 
• Modeled Residue Count: 375 
• Deposited Residue Count: 428 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate kinase	A, B	214	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: tmk, Rv3247c EC: 2.7.4.9
UniProt
Find proteins for P9WKE1 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WKE1  Go to UniProtKB:  P9WKE1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZUI	C [auth A], G [auth B]	1-[1-[[5-(3-chloranylphenoxy)pyridin-3-yl]methyl]piperidin-4-yl]-5-methyl-pyrimidine-2,4-dione C22 H23 Cl N4 O3 RNTPQXGZOHDUAY-UHFFFAOYSA-N
CL	D [auth A], E [auth A], F [auth A], H [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
ZUI	BindingDB:  5NRQ	IC50: 770 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.210 (Depositor), 0.214 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.85	α = 90
b = 73.85	β = 90
c = 72.35	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Merceron, R., Song, L., Munier-Lehmann, H., Van Calenbergh, S., Savvides, S.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description