8JXN

Human 3-methylcrotonyl-CoA carboxylase in BCCP-H1 state with MCoA

PDB DOI: https://doi.org/10.2210/pdb8JXN/pdb
EM Map EMD-36706: 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: 3.20 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 BCCP-H1 state with substrate

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

To be published.

Macromolecule Content

Total Structure Weight: 858.41 kDa
Atom Count: 51,216
Modelled Residue Count: 6,582
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 D] D [auth G] G [auth I] J [auth B] K A [auth D], D [auth G], G [auth I], J [auth B], K, L [auth A]	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 E] C [auth F] E [auth H] F [auth C] H [auth J] B [auth E], C [auth F], E [auth H], F [auth C], H [auth J], I [auth L]	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 N [auth D] SDF format, chain R [auth G] SDF format, chain S [auth I] SDF format, chain V [auth B] SDF format, chain W [auth K] SDF format, chain X [auth A] MOL2 format, chain N [auth D] MOL2 format, chain R [auth G] MOL2 format, chain S [auth I] MOL2 format, chain V [auth B] MOL2 format, chain W [auth K] MOL2 format, chain X [auth A]	N [auth D] R [auth G] S [auth I] V [auth B] W [auth K] N [auth D], R [auth G], S [auth I], V [auth B], W [auth K], X [auth A]	~{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 N [auth D] Focus chain R [auth G] Focus chain S [auth I] Focus chain V [auth B] Focus chain W [auth K] Focus chain X [auth A] Interactions & Density Focus chain N [auth D] Focus chain R [auth G] Focus chain S [auth I] Focus chain V [auth B] Focus chain W [auth K] Focus chain X [auth A]
BTI Query on BTI Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain O [auth E] SDF format, chain P [auth F] SDF format, chain Q [auth G] SDF format, chain T [auth I] SDF format, chain U [auth B] MOL2 format, chain M [auth D] MOL2 format, chain O [auth E] MOL2 format, chain P [auth F] MOL2 format, chain Q [auth G] MOL2 format, chain T [auth I] MOL2 format, chain U [auth B]	M [auth D] O [auth E] P [auth F] Q [auth G] T [auth I] M [auth D], O [auth E], P [auth F], Q [auth G], T [auth I], U [auth B]	5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL C₁₀ H₁₆ N₂ O₂ S ARDNWGMSCXSPBF-CIUDSAMLSA-N		Interactions Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain T [auth I] Focus chain U [auth B] Interactions & Density Focus chain M [auth D] Focus chain O [auth E] Focus chain P [auth F] Focus chain Q [auth G] Focus chain T [auth I] Focus chain U [auth B]