8F8K

The structure of Rv2173 from M. tuberculosis with IPP bound

PDB DOI: https://doi.org/10.2210/pdb8F8K/pdb

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

Deposited: 2022-11-22 Released: 2023-11-29
Deposition Author(s): Johnston, J.M., Allison, T.M., Titterington, J., Beasley, C.P.H.
Funding Organization(s): Ministry of Business, Innovation and Employment (New Zealand)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.239
R-Value Work: 0.208
R-Value Observed: 0.210

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

The structure of Rv2173 from M. tuberculosis in APO-, IPP-, and DMAP-bound forms.

Johnston, J.M., Allison, T.M., Titterington, J., Beasley, C.P.H.

To be published.

Macromolecule Content

Total Structure Weight: 42.8 kDa
Atom Count: 2,806
Modelled Residue Count: 353
Deposited Residue Count: 387
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
(2E,6E)-farnesyl diphosphate synthase	A	387	Mycobacterium tuberculosis	Mutation(s): 0 Gene Names: idsA2
UniProt
Find proteins for O53507 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53507 Go to UniProtKB: O53507
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O53507
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IPE (Subject of Investigation/LOI) Query on IPE Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	3-METHYLBUT-3-ENYL TRIHYDROGEN DIPHOSPHATE C₅ H₁₂ O₇ P₂ NUHSROFQTUXZQQ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain H [auth A] MOL2 format, chain B [auth A] MOL2 format, chain H [auth A]	B [auth A], H [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain H [auth A] Interactions & Density Focus chain B [auth A] Focus chain H [auth A]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A]	C [auth A], D [auth A], E [auth A], G [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A]	I [auth A], J [auth A], K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain L [auth A] MOL2 format, chain L [auth A]	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain L [auth A] Interactions & Density Focus chain L [auth A]