9YX4 | pdb_00009yx4

Structure of the long chain acyl-CoA carboxylase complex from Mycobacterium smegmatis with ATP, bicarbonate, arachidoyl-CoA, and propionyl-CoA

PDB DOI: https://doi.org/10.2210/pdb9YX4/pdb
EM Map EMD-73595: 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: 2.30 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: 1,137.33 kDa
Atom Count: 56,623
Modeled Residue Count: 7,663
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
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], O [auth B], P [auth D], Q [auth C], R [auth T], S [auth R], T [auth S]	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: 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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(by identity cutoff) | 3D Structure

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
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
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 Y [auth F] SDF format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F]	Y [auth F], Z [auth F]	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 Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain Y [auth F] Focus chain Z [auth F]
1VU (Subject of Investigation/LOI) Query on 1VU Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth H] SDF format, chain GA [auth M] SDF format, chain HA [auth N] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain GA [auth M] MOL2 format, chain HA [auth N] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain GA [auth M] mmCIF format, chain HA [auth N]	AA [auth G], BA [auth H], GA [auth M], HA [auth N]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain AA [auth G] Focus chain BA [auth H] Focus chain GA [auth M] Focus chain HA [auth N] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth H] Focus chain GA [auth M] Focus chain HA [auth N]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain BB [auth S] SDF format, chain KA [auth Q] SDF format, chain MA [auth B] SDF format, chain PA [auth D] SDF format, chain SA [auth C] SDF format, chain VA [auth T] SDF format, chain W [auth A] SDF format, chain YA [auth R] MOL2 format, chain BB [auth S] MOL2 format, chain KA [auth Q] MOL2 format, chain MA [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain VA [auth T] MOL2 format, chain W [auth A] MOL2 format, chain YA [auth R] mmCIF format, chain BB [auth S] mmCIF format, chain KA [auth Q] mmCIF format, chain MA [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain SA [auth C] mmCIF format, chain VA [auth T] mmCIF format, chain W [auth A] mmCIF format, chain YA [auth R]	BB [auth S] KA [auth Q] MA [auth B] PA [auth D] SA [auth C] BB [auth S], KA [auth Q], MA [auth B], PA [auth D], SA [auth C], VA [auth T], W [auth A], YA [auth R]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BB [auth S] Focus chain KA [auth Q] Focus chain MA [auth B] Focus chain PA [auth D] Focus chain SA [auth C] Focus chain VA [auth T] Focus chain W [auth A] Focus chain YA [auth R] Interactions & Density Focus chain BB [auth S] Focus chain KA [auth Q] Focus chain MA [auth B] Focus chain PA [auth D] Focus chain SA [auth C] Focus chain VA [auth T] Focus chain W [auth A] Focus chain YA [auth R]
BTN (Subject of Investigation/LOI) Query on BTN Download Ideal Coordinates CCD File SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth K] SDF format, chain FA [auth L] SDF format, chain IA [auth Q] SDF format, chain U [auth A] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth K] MOL2 format, chain FA [auth L] MOL2 format, chain IA [auth Q] MOL2 format, chain U [auth A] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth K] mmCIF format, chain FA [auth L] mmCIF format, chain IA [auth Q] mmCIF format, chain U [auth A]	CA [auth I] DA [auth J] EA [auth K] FA [auth L] IA [auth Q] CA [auth I], DA [auth J], EA [auth K], FA [auth L], IA [auth Q], U [auth A]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain IA [auth Q] Focus chain U [auth A] Interactions & Density Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth K] Focus chain FA [auth L] Focus chain IA [auth Q] Focus chain U [auth A]
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain AB [auth R] SDF format, chain DB [auth S] SDF format, chain JA [auth Q] SDF format, chain OA [auth B] SDF format, chain RA [auth D] SDF format, chain UA [auth C] SDF format, chain V [auth A] SDF format, chain WA [auth T] MOL2 format, chain AB [auth R] MOL2 format, chain DB [auth S] MOL2 format, chain JA [auth Q] MOL2 format, chain OA [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain UA [auth C] MOL2 format, chain V [auth A] MOL2 format, chain WA [auth T] mmCIF format, chain AB [auth R] mmCIF format, chain DB [auth S] mmCIF format, chain JA [auth Q] mmCIF format, chain OA [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain UA [auth C] mmCIF format, chain V [auth A] mmCIF format, chain WA [auth T]	AB [auth R] DB [auth S] JA [auth Q] OA [auth B] RA [auth D] AB [auth R], DB [auth S], JA [auth Q], OA [auth B], RA [auth D], UA [auth C], V [auth A], WA [auth T]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain AB [auth R] Focus chain DB [auth S] Focus chain JA [auth Q] Focus chain OA [auth B] Focus chain RA [auth D] Focus chain UA [auth C] Focus chain V [auth A] Focus chain WA [auth T] Interactions & Density Focus chain AB [auth R] Focus chain DB [auth S] Focus chain JA [auth Q] Focus chain OA [auth B] Focus chain RA [auth D] Focus chain UA [auth C] Focus chain V [auth A] Focus chain WA [auth T]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain CB [auth S] SDF format, chain LA [auth Q] SDF format, chain NA [auth B] SDF format, chain QA [auth D] SDF format, chain TA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth T] SDF format, chain ZA [auth R] MOL2 format, chain CB [auth S] MOL2 format, chain LA [auth Q] MOL2 format, chain NA [auth B] MOL2 format, chain QA [auth D] MOL2 format, chain TA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth T] MOL2 format, chain ZA [auth R] mmCIF format, chain CB [auth S] mmCIF format, chain LA [auth Q] mmCIF format, chain NA [auth B] mmCIF format, chain QA [auth D] mmCIF format, chain TA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth T] mmCIF format, chain ZA [auth R]	CB [auth S] LA [auth Q] NA [auth B] QA [auth D] TA [auth C] CB [auth S], LA [auth Q], NA [auth B], QA [auth D], TA [auth C], X [auth A], XA [auth T], ZA [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CB [auth S] Focus chain LA [auth Q] Focus chain NA [auth B] Focus chain QA [auth D] Focus chain TA [auth C] Focus chain X [auth A] Focus chain XA [auth T] Focus chain ZA [auth R] Interactions & Density Focus chain CB [auth S] Focus chain LA [auth Q] Focus chain NA [auth B] Focus chain QA [auth D] Focus chain TA [auth C] Focus chain X [auth A] Focus chain XA [auth T] Focus chain ZA [auth R]