9YX2 | pdb_00009yx2

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

PDB DOI: https://doi.org/10.2210/pdb9YX2/pdb
EM Map EMD-73585: 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: 2.80 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: 1,135.22 kDa
Atom Count: 54,893
Modeled Residue Count: 7,657
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, B, C, D, I A, B, C, D, I, J, K, L, Q, R, S, 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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-/propionyl-coenzyme A carboxylase AccE5	E, 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	F, 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	G, H, M, 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1VU (Subject of Investigation/LOI) Query on 1VU Download Ideal Coordinates CCD File SDF format, chain HA [auth G] SDF format, chain KA [auth H] SDF format, chain JA [auth H] SDF format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain IA [auth G]	HA [auth G], IA [auth G], JA [auth H], KA [auth H]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth H] Interactions & Density Focus chain HA [auth G] Focus chain IA [auth G] Focus chain JA [auth H] Focus chain KA [auth H]
ATP (Subject of Investigation/LOI) Query on ATP Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain W [auth A] SDF format, chain ZA [auth T] SDF format, chain Y [auth B] SDF format, chain WA [auth S] SDF format, chain TA [auth R] SDF format, chain RA [auth Q] SDF format, chain BA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain ZA [auth T] MOL2 format, chain Y [auth B] MOL2 format, chain WA [auth S] MOL2 format, chain TA [auth R] MOL2 format, chain RA [auth Q] MOL2 format, chain BA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain ZA [auth T] mmCIF format, chain Y [auth B] mmCIF format, chain WA [auth S] mmCIF format, chain TA [auth R] mmCIF format, chain RA [auth Q] mmCIF format, chain BA [auth C]	BA [auth C] EA [auth D] RA [auth Q] TA [auth R] W [auth A] BA [auth C], EA [auth D], RA [auth Q], TA [auth R], W [auth A], WA [auth S], Y [auth B], ZA [auth T]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain BA [auth C] Focus chain EA [auth D] Focus chain RA [auth Q] Focus chain TA [auth R] Focus chain W [auth A] Focus chain WA [auth S] Focus chain Y [auth B] Focus chain ZA [auth T] Interactions & Density Focus chain BA [auth C] Focus chain EA [auth D] Focus chain RA [auth Q] Focus chain TA [auth R] Focus chain W [auth A] Focus chain WA [auth S] Focus chain Y [auth B] Focus chain ZA [auth T]
BTN (Subject of Investigation/LOI) Query on BTN Download Ideal Coordinates CCD File SDF format, chain LA [auth I] SDF format, chain MA [auth J] SDF format, chain PA [auth Q] SDF format, chain U [auth A] SDF format, chain OA [auth L] SDF format, chain NA [auth K] MOL2 format, chain LA [auth I] MOL2 format, chain MA [auth J] MOL2 format, chain PA [auth Q] MOL2 format, chain U [auth A] MOL2 format, chain OA [auth L] MOL2 format, chain NA [auth K] mmCIF format, chain LA [auth I] mmCIF format, chain MA [auth J] mmCIF format, chain PA [auth Q] mmCIF format, chain U [auth A] mmCIF format, chain OA [auth L] mmCIF format, chain NA [auth K]	LA [auth I] MA [auth J] NA [auth K] OA [auth L] PA [auth Q] LA [auth I], MA [auth J], NA [auth K], OA [auth L], PA [auth Q], U [auth A]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain LA [auth I] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth Q] Focus chain U [auth A] Interactions & Density Focus chain LA [auth I] Focus chain MA [auth J] Focus chain NA [auth K] Focus chain OA [auth L] Focus chain PA [auth Q] Focus chain U [auth A]
BCT (Subject of Investigation/LOI) Query on BCT Download Ideal Coordinates CCD File SDF format, chain QA [auth Q] SDF format, chain V [auth A] SDF format, chain VA [auth R] SDF format, chain YA [auth S] SDF format, chain GA [auth D] SDF format, chain DA [auth C] SDF format, chain AB [auth T] SDF format, chain AA [auth B] MOL2 format, chain QA [auth Q] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth R] MOL2 format, chain YA [auth S] MOL2 format, chain GA [auth D] MOL2 format, chain DA [auth C] MOL2 format, chain AB [auth T] MOL2 format, chain AA [auth B] mmCIF format, chain QA [auth Q] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth R] mmCIF format, chain YA [auth S] mmCIF format, chain GA [auth D] mmCIF format, chain DA [auth C] mmCIF format, chain AB [auth T] mmCIF format, chain AA [auth B]	AA [auth B] AB [auth T] DA [auth C] GA [auth D] QA [auth Q] AA [auth B], AB [auth T], DA [auth C], GA [auth D], QA [auth Q], V [auth A], VA [auth R], YA [auth S]	BICARBONATE ION C H O₃ BVKZGUZCCUSVTD-UHFFFAOYSA-M		Interactions Focus chain AA [auth B] Focus chain AB [auth T] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain QA [auth Q] Focus chain V [auth A] Focus chain VA [auth R] Focus chain YA [auth S] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth T] Focus chain DA [auth C] Focus chain GA [auth D] Focus chain QA [auth Q] Focus chain V [auth A] Focus chain VA [auth R] Focus chain YA [auth S]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain XA [auth S] SDF format, chain Z [auth B] SDF format, chain X [auth A] SDF format, chain UA [auth R] SDF format, chain SA [auth Q] SDF format, chain FA [auth D] SDF format, chain CA [auth C] SDF format, chain BB [auth T] MOL2 format, chain XA [auth S] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth A] MOL2 format, chain UA [auth R] MOL2 format, chain SA [auth Q] MOL2 format, chain FA [auth D] MOL2 format, chain CA [auth C] MOL2 format, chain BB [auth T] mmCIF format, chain XA [auth S] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth A] mmCIF format, chain UA [auth R] mmCIF format, chain SA [auth Q] mmCIF format, chain FA [auth D] mmCIF format, chain CA [auth C] mmCIF format, chain BB [auth T]	BB [auth T] CA [auth C] FA [auth D] SA [auth Q] UA [auth R] BB [auth T], CA [auth C], FA [auth D], SA [auth Q], UA [auth R], X [auth A], XA [auth S], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain BB [auth T] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain SA [auth Q] Focus chain UA [auth R] Focus chain X [auth A] Focus chain XA [auth S] Focus chain Z [auth B] Interactions & Density Focus chain BB [auth T] Focus chain CA [auth C] Focus chain FA [auth D] Focus chain SA [auth Q] Focus chain UA [auth R] Focus chain X [auth A] Focus chain XA [auth S] Focus chain Z [auth B]