9YX5 | pdb_00009yx5

Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with MSMEG_0435-MSMEG_0436 bound

PDB DOI: https://doi.org/10.2210/pdb9YX5/pdb
EM Map EMD-73596: 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: 2.90 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: 1,367.84 kDa
Atom Count: 56,321
Modeled Residue Count: 8,786
Deposited Residue Count: 12,770
Unique protein chains: 6

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Biotin-dependent acyl-coenzyme A carboxylase alpha3 subunit	A F [auth I] G [auth J] H [auth K] I [auth L] A, F [auth I], G [auth J], H [auth K], I [auth L], N [auth Q], Q [auth X], T [auth U], U [auth B], V [auth C], W [auth D], X [auth R], Y [auth S], Z [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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-/propionyl-coenzyme A carboxylase AccE5	B [auth E], M [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

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	C [auth F], L [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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain	D [auth G], E [auth H], J [auth M], K [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
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophanate hydrolase subunit 2	O [auth V], R [auth Y]	294	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QPL0 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL0 Go to UniProtKB: A0QPL0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QPL0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Allophanate hydrolase subunit 1	P [auth W], S [auth Z]	210	Mycolicibacterium smegmatis MC2 155	Mutation(s): 0
UniProt
Find proteins for A0QPL1 (Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)) Explore A0QPL1 Go to UniProtKB: A0QPL1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0QPL1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CZD (Subject of Investigation/LOI) Query on A1CZD Download Ideal Coordinates CCD File SDF format, chain HA [auth O] SDF format, chain AA [auth F] MOL2 format, chain HA [auth O] MOL2 format, chain AA [auth F] mmCIF format, chain HA [auth O] mmCIF format, chain AA [auth F]	AA [auth F], HA [auth O]	S-{(3S,5S,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5,10,14-tetraoxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (11E,14E,16E)-icosa-11,14,16-trienethioate (non-preferred name) C₄₁ H₆₈ N₇ O₁₇ P₃ S VXJQAOBDWILAOY-WVXUJWCUSA-N		Interactions Focus chain AA [auth F] Focus chain HA [auth O] Interactions & Density Focus chain AA [auth F] Focus chain HA [auth O]
1VU (Subject of Investigation/LOI) Query on 1VU Download Ideal Coordinates CCD File SDF format, chain GA [auth N] SDF format, chain FA [auth M] SDF format, chain CA [auth H] SDF format, chain BA [auth G] MOL2 format, chain GA [auth N] MOL2 format, chain FA [auth M] MOL2 format, chain CA [auth H] MOL2 format, chain BA [auth G] mmCIF format, chain GA [auth N] mmCIF format, chain FA [auth M] mmCIF format, chain CA [auth H] mmCIF format, chain BA [auth G]	BA [auth G], CA [auth H], FA [auth M], GA [auth N]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain BA [auth G] Focus chain CA [auth H] Focus chain FA [auth M] Focus chain GA [auth N] Interactions & Density Focus chain BA [auth G] Focus chain CA [auth H] Focus chain FA [auth M] Focus chain GA [auth N]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain OA [auth R] SDF format, chain KA [auth Q] MOL2 format, chain OA [auth R] MOL2 format, chain KA [auth Q] mmCIF format, chain OA [auth R] mmCIF format, chain KA [auth Q]	KA [auth Q], OA [auth R]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain KA [auth Q] Focus chain OA [auth R] Interactions & Density Focus chain KA [auth Q] Focus chain OA [auth R]
BTN (Subject of Investigation/LOI) Query on BTN Download Ideal Coordinates CCD File SDF format, chain NA [auth U] SDF format, chain MA [auth X] SDF format, chain IA [auth Q] SDF format, chain EA [auth K] SDF format, chain DA [auth I] MOL2 format, chain NA [auth U] MOL2 format, chain MA [auth X] MOL2 format, chain IA [auth Q] MOL2 format, chain EA [auth K] MOL2 format, chain DA [auth I] mmCIF format, chain NA [auth U] mmCIF format, chain MA [auth X] mmCIF format, chain IA [auth Q] mmCIF format, chain EA [auth K] mmCIF format, chain DA [auth I]	DA [auth I], EA [auth K], IA [auth Q], MA [auth X], NA [auth U]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain DA [auth I] Focus chain EA [auth K] Focus chain IA [auth Q] Focus chain MA [auth X] Focus chain NA [auth U] Interactions & Density Focus chain DA [auth I] Focus chain EA [auth K] Focus chain IA [auth Q] Focus chain MA [auth X] Focus chain NA [auth U]
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain QA [auth R] SDF format, chain JA [auth Q] MOL2 format, chain QA [auth R] MOL2 format, chain JA [auth Q] mmCIF format, chain QA [auth R] mmCIF format, chain JA [auth Q]	JA [auth Q], QA [auth R]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain JA [auth Q] Focus chain QA [auth R] Interactions & Density Focus chain JA [auth Q] Focus chain QA [auth R]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain PA [auth R] SDF format, chain LA [auth Q] MOL2 format, chain PA [auth R] MOL2 format, chain LA [auth Q] mmCIF format, chain PA [auth R] mmCIF format, chain LA [auth Q]	LA [auth Q], PA [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain LA [auth Q] Focus chain PA [auth R] Interactions & Density Focus chain LA [auth Q] Focus chain PA [auth R]