8XL5

Structure of human propionyl-CoA carboxylase in complex with propionyl-CoA (PCC-PCO)

PDB DOI: https://doi.org/10.2210/pdb8XL5/pdb
EM Map EMD-38438: EMDB EMDataResource

Classification: LIGASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2023-12-25 Released: 2024-10-30
Deposition Author(s): Zhou, F.Y., Zhang, Y.Y., Zhou, Q., Hu, Q.
Funding Organization(s): Not funded

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 1.1 of the entry. See complete history.

Literature

Structural insights into human propionyl-CoA carboxylase (PCC) and 3-methylcrotonyl-CoA carboxylase (MCC)

Zhou, F., Zhang, Y., Zhu, Y., Zhou, Q., Shi, Y., Hu, Q.

(2024) Elife

DOI: https://doi.org/10.7554/elife.98885.2

Macromolecule Content

Total Structure Weight: 837.09 kDa
Atom Count: 54,522
Modelled Residue Count: 7,050
Deposited Residue Count: 7,602
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase alpha chain, mitochondrial	A, C, E, G, I A, C, E, G, I, K	728	Homo sapiens	Mutation(s): 0 EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05165 (Homo sapiens) Explore P05165 Go to UniProtKB: P05165
PHAROS: P05165 GTEx: ENSG00000175198
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05165
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Propionyl-CoA carboxylase beta chain, mitochondrial	B, D, F, H, J B, D, F, H, J, L	539	Homo sapiens	Mutation(s): 0 EC: 6.4.1.3
UniProt & NIH Common Fund Data Resources
Find proteins for P05166 (Homo sapiens) Explore P05166 Go to UniProtKB: P05166
PHAROS: P05166 GTEx: ENSG00000114054
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P05166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 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 N [auth B] SDF format, chain P [auth D] SDF format, chain R [auth F] SDF format, chain T [auth H] SDF format, chain V [auth J] SDF format, chain X [auth L] MOL2 format, chain N [auth B] MOL2 format, chain P [auth D] MOL2 format, chain R [auth F] MOL2 format, chain T [auth H] MOL2 format, chain V [auth J] MOL2 format, chain X [auth L] mmCIF format, chain N [auth B] mmCIF format, chain P [auth D] mmCIF format, chain R [auth F] mmCIF format, chain T [auth H] mmCIF format, chain V [auth J] mmCIF format, chain X [auth L]	N [auth B] P [auth D] R [auth F] T [auth H] V [auth J] N [auth B], P [auth D], R [auth F], T [auth H], V [auth J], X [auth L]	propionyl Coenzyme A C₂₄ H₄₀ N₇ O₁₇ P₃ S QAQREVBBADEHPA-IEXPHMLFSA-N		Interactions Focus chain N [auth B] Focus chain P [auth D] Focus chain R [auth F] Focus chain T [auth H] Focus chain V [auth J] Focus chain X [auth L] Interactions & Density Focus chain N [auth B] Focus chain P [auth D] Focus chain R [auth F] Focus chain T [auth H] Focus chain V [auth J] Focus chain X [auth L]
BTN (Subject of Investigation/LOI) Query on BTN Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth C] SDF format, chain Q [auth E] SDF format, chain S [auth G] SDF format, chain U [auth I] SDF format, chain W [auth K] MOL2 format, chain M [auth A] MOL2 format, chain O [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain S [auth G] MOL2 format, chain U [auth I] MOL2 format, chain W [auth K] mmCIF format, chain M [auth A] mmCIF format, chain O [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain S [auth G] mmCIF format, chain U [auth I] mmCIF format, chain W [auth K]	M [auth A] O [auth C] Q [auth E] S [auth G] U [auth I] M [auth A], O [auth C], Q [auth E], S [auth G], U [auth I], W [auth K]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth E] Focus chain S [auth G] Focus chain U [auth I] Focus chain W [auth K] Interactions & Density Focus chain M [auth A] Focus chain O [auth C] Focus chain Q [auth E] Focus chain S [auth G] Focus chain U [auth I] Focus chain W [auth K]