5NRN | pdb_00005nrn

Mtb TMK crystal structure in complex with compound 3

PDB DOI: https://doi.org/10.2210/pdb5NRN/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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.199 (Depositor), 0.212 (DCC)
R-Value Work:
0.172 (Depositor), 0.187 (DCC)
R-Value Observed:
0.173 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Mtb TMK crystal structure in complex with compound LS3080

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

To be published.

Macromolecule Content

Total Structure Weight: 46.36 kDa
Atom Count: 3,301
Modeled Residue Count: 398
Deposited Residue Count: 428
Unique protein chains: 1

Macromolecules

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| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P9WKE1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
95W Query on 95W Download:Ideal Coordinates CCD File SDF format, chain G [auth B] SDF format, chain C [auth A] MOL2 format, chain G [auth B] MOL2 format, chain C [auth A] mmCIF format, chain G [auth B] mmCIF format, chain C [auth A]	C [auth A], G [auth B]	5-methyl-1-[1-[(6-phenoxypyridin-2-yl)methyl]piperidin-4-yl]pyrimidine-2,4-dione C₂₂ H₂₄ N₄ O₃ BKRRWLAIGUKKJX-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]