8JXM

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H2 state with MCoA

PDB DOI: https://doi.org/10.2210/pdb8JXM/pdb
EM Map EMD-36705: EMDB EMDataResource

Classification: CYTOSOLIC PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2023-06-30 Released: 2024-07-03
Deposition Author(s): Liu, D.S., Su, J.Y., Tian, X.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.49 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

Human 3-methylcrotonyl-CoA carboxylase in

Liu, D.S., Su, J.Y.

To be published.

Macromolecule Content

Total Structure Weight: 858.41 kDa
Atom Count: 51,993
Modelled Residue Count: 6,678
Deposited Residue Count: 7,728
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial	A [auth K] C [auth A] E [auth C] H K [auth E] A [auth K], C [auth A], E [auth C], H, K [auth E], L [auth J]	563	Homo sapiens	Mutation(s): 0 Gene Names: MCCC2, MCCB EC: 6.4.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9HCC0 (Homo sapiens) Explore Q9HCC0 Go to UniProtKB: Q9HCC0
PHAROS: Q9HCC0 GTEx: ENSG00000131844
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9HCC0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial	B [auth L] D [auth B] F G I B [auth L], D [auth B], F, G, I, J [auth M]	725	Homo sapiens	Mutation(s): 0 Gene Names: MCCC1, MCCA EC: 6.4.1.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q96RQ3 (Homo sapiens) Explore Q96RQ3 Go to UniProtKB: Q96RQ3
PHAROS: Q96RQ3 GTEx: ENSG00000078070
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96RQ3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
TW3 (Subject of Investigation/LOI) Query on TW3 Download Ideal Coordinates CCD File SDF format, chain M [auth K] SDF format, chain N [auth A] SDF format, chain P [auth C] SDF format, chain T [auth H] SDF format, chain W [auth E] SDF format, chain X [auth J] MOL2 format, chain M [auth K] MOL2 format, chain N [auth A] MOL2 format, chain P [auth C] MOL2 format, chain T [auth H] MOL2 format, chain W [auth E] MOL2 format, chain X [auth J] mmCIF format, chain M [auth K] mmCIF format, chain N [auth A] mmCIF format, chain P [auth C] mmCIF format, chain T [auth H] mmCIF format, chain W [auth E] mmCIF format, chain X [auth J]	M [auth K] N [auth A] P [auth C] T [auth H] W [auth E] M [auth K], N [auth A], P [auth C], T [auth H], W [auth E], X [auth J]	~{S}-[2-[3-[[(2~{R})-4-[[[(2~{S},3~{S},4~{S},5~{S})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethyl] 3-methylbut-2-enethioate C₂₆ H₄₂ N₇ O₁₇ P₃ S BXIPALATIYNHJN-XDPCYSMHSA-N		Interactions Focus chain M [auth K] Focus chain N [auth A] Focus chain P [auth C] Focus chain T [auth H] Focus chain W [auth E] Focus chain X [auth J] Interactions & Density Focus chain M [auth K] Focus chain N [auth A] Focus chain P [auth C] Focus chain T [auth H] Focus chain W [auth E] Focus chain X [auth J]
BTI Query on BTI Download Ideal Coordinates CCD File SDF format, chain O [auth C] SDF format, chain Q [auth F] SDF format, chain R [auth G] SDF format, chain S [auth H] SDF format, chain U [auth I] SDF format, chain V [auth M] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth G] MOL2 format, chain S [auth H] MOL2 format, chain U [auth I] MOL2 format, chain V [auth M] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth F] mmCIF format, chain R [auth G] mmCIF format, chain S [auth H] mmCIF format, chain U [auth I] mmCIF format, chain V [auth M]	O [auth C] Q [auth F] R [auth G] S [auth H] U [auth I] O [auth C], Q [auth F], R [auth G], S [auth H], U [auth I], V [auth M]	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL C₁₀ H₁₆ N₂ O₂ S ARDNWGMSCXSPBF-CIUDSAMLSA-N		Interactions Focus chain O [auth C] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain V [auth M] Interactions & Density Focus chain O [auth C] Focus chain Q [auth F] Focus chain R [auth G] Focus chain S [auth H] Focus chain U [auth I] Focus chain V [auth M]