8J4Z

Human 3-methylcrotonyl-CoA carboxylase in BCCP-CTS state with substrate

PDB DOI: https://doi.org/10.2210/pdb8J4Z/pdb
EM Map EMD-35980: EMDB EMDataResource

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

Deposited: 2023-04-21 Released: 2024-04-24
Deposition Author(s): Liu, D.S., Su, J.Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.73 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-CTS state with substrate

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

To be published.

Macromolecule Content

Total Structure Weight: 858.41 kDa
Atom Count: 53,664
Modelled Residue Count: 6,906
Deposited Residue Count: 7,728
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methylcrotonoyl-CoA carboxylase beta chain, mitochondrial	A [auth J] C [auth A] E [auth C] G [auth F] I [auth H] A [auth J], C [auth A], E [auth C], G [auth F], I [auth H], K	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] D [auth B] F [auth D] H [auth G] J [auth I] B [auth E], D [auth B], F [auth D], H [auth G], J [auth I], 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 Query on TW3 Download Ideal Coordinates CCD File SDF format, chain N [auth J] SDF format, chain P [auth A] SDF format, chain R [auth C] SDF format, chain S [auth F] SDF format, chain U [auth H] SDF format, chain W [auth K] MOL2 format, chain N [auth J] MOL2 format, chain P [auth A] MOL2 format, chain R [auth C] MOL2 format, chain S [auth F] MOL2 format, chain U [auth H] MOL2 format, chain W [auth K]	N [auth J] P [auth A] R [auth C] S [auth F] U [auth H] N [auth J], P [auth A], R [auth C], S [auth F], U [auth H], W [auth K]	~{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 J] Focus chain P [auth A] Focus chain R [auth C] Focus chain S [auth F] Focus chain U [auth H] Focus chain W [auth K] Interactions & Density Focus chain N [auth J] Focus chain P [auth A] Focus chain R [auth C] Focus chain S [auth F] Focus chain U [auth H] Focus chain W [auth K]
BTI Query on BTI Download Ideal Coordinates CCD File SDF format, chain M [auth J] SDF format, chain O [auth A] SDF format, chain Q [auth C] SDF format, chain T [auth F] SDF format, chain V [auth H] SDF format, chain X [auth K] MOL2 format, chain M [auth J] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth C] MOL2 format, chain T [auth F] MOL2 format, chain V [auth H] MOL2 format, chain X [auth K]	M [auth J] O [auth A] Q [auth C] T [auth F] V [auth H] M [auth J], O [auth A], Q [auth C], T [auth F], V [auth H], X [auth K]	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 J] Focus chain O [auth A] Focus chain Q [auth C] Focus chain T [auth F] Focus chain V [auth H] Focus chain X [auth K] Interactions & Density Focus chain M [auth J] Focus chain O [auth A] Focus chain Q [auth C] Focus chain T [auth F] Focus chain V [auth H] Focus chain X [auth K]