9OJN | pdb_00009ojn

Structure of Mycobacterium smegmatis EtfD

PDB DOI: https://doi.org/10.2210/pdb9OJN/pdb
EM Map EMD-70545: EMDB EMDataResource

Classification: OXIDOREDUCTASE
Organism(s): Mycolicibacterium smegmatis MC2 155
Mutation(s): No

Deposited: 2025-05-08 Released: 2025-05-21
Deposition Author(s): Courbon, G.M., Rubinstein, J.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.20 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Mycobacterial EtfD contains an unusual linear [3Fe-4S] cluster and enables beta oxidation to drive proton pumping by the electron transport chain

Courbon, G.M., Rubinstein, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 114.31 kDa
Atom Count: 5,601
Modeled Residue Count: 742
Deposited Residue Count: 1,042
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Iron-sulfur-binding reductase	A	1,042	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for I7FE09 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore I7FE09 Go to UniProtKB: I7FE09
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I7FE09
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MQ9 (Subject of Investigation/LOI) Query on MQ9 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MENAQUINONE-9 C₅₆ H₈₀ O₂ WCRXHNIUHQUASO-ABFXHILCSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
HEM (Subject of Investigation/LOI) Query on HEM Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
LMT (Subject of Investigation/LOI) Query on LMT Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
9S8 (Subject of Investigation/LOI) Query on 9S8 Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	Non-cubane [4Fe-4S]-cluster Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SF4 (Subject of Investigation/LOI) Query on SF4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A]	E [auth A], F [auth A]	IRON/SULFUR CLUSTER Fe₄ S₄ LJBDFODJNLIPKO-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A]
A1CBX (Subject of Investigation/LOI) Query on A1CBX Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	1,3,5,7-tetrathia-2$l^{2},4$l^{4},6$l^{2}-triferraspiro[3.3]heptane Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]