9YX1 | pdb_00009yx1

Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis

PDB DOI: https://doi.org/10.2210/pdb9YX1/pdb
EM Map EMD-73575: EMDB EMDataResource

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

Deposited: 2025-10-26 Released: 2025-11-26
Deposition Author(s): Liang, Y., Rubinstein, J.L.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 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

Structural basis for substrate specificity and MSMEG_0435-0436 binding by the mycobacterial long-chain acyl-CoA carboxylase complex

Liang, Y., Rubinstein, J.L.

To be published.

Macromolecule Content

Total Structure Weight: 1,127.31 kDa
Atom Count: 48,731
Modeled Residue Count: 7,040
Deposited Residue Count: 10,566
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	A [auth F], G [auth O]	517	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.4.1.3
UniProt
Find proteins for A0R616 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0R616 Go to UniProtKB: A0R616
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0R616
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	B [auth G], C [auth H], E [auth M], F [auth N]	542	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.4.1.3
UniProt
Find proteins for A0QTE7 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE7 Go to UniProtKB: A0QTE7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QTE7
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit	D [auth K] H [auth I] I [auth J] J [auth L] K [auth A] D [auth K], H [auth I], I [auth J], J [auth L], K [auth A], L [auth D], M [auth B], N [auth C], P [auth Q], Q [auth S], R, S [auth T]	598	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0 EC: 6.3.4.14
UniProt
Find proteins for A0QTE1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE1 Go to UniProtKB: A0QTE1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QTE1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-/propionyl-coenzyme A carboxylase AccE5	O [auth E], T [auth P]	94	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QTE6 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QTE6 Go to UniProtKB: A0QTE6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QTE6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN (Subject of Investigation/LOI) Query on BTN Download Ideal Coordinates CCD File SDF format, chain AA [auth Q] SDF format, chain U [auth K] SDF format, chain V [auth I] SDF format, chain W [auth J] SDF format, chain X [auth L] SDF format, chain Y [auth A] MOL2 format, chain AA [auth Q] MOL2 format, chain U [auth K] MOL2 format, chain V [auth I] MOL2 format, chain W [auth J] MOL2 format, chain X [auth L] MOL2 format, chain Y [auth A] mmCIF format, chain AA [auth Q] mmCIF format, chain U [auth K] mmCIF format, chain V [auth I] mmCIF format, chain W [auth J] mmCIF format, chain X [auth L] mmCIF format, chain Y [auth A]	AA [auth Q] U [auth K] V [auth I] W [auth J] X [auth L] AA [auth Q], U [auth K], V [auth I], W [auth J], X [auth L], Y [auth A]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain AA [auth Q] Focus chain U [auth K] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth L] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth Q] Focus chain U [auth K] Focus chain V [auth I] Focus chain W [auth J] Focus chain X [auth L] Focus chain Y [auth A]
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain BA [auth Q] SDF format, chain Z [auth A] MOL2 format, chain BA [auth Q] MOL2 format, chain Z [auth A] mmCIF format, chain BA [auth Q] mmCIF format, chain Z [auth A]	BA [auth Q], Z [auth A]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain BA [auth Q] Focus chain Z [auth A] Interactions & Density Focus chain BA [auth Q] Focus chain Z [auth A]