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Crystal structure of the carboxyltransferase subunit of acc (ACCD6) in complex with inhibitor quizalofop-P derivative from mycobacterium tuberculosis

Analyse Crystal structure of the carboxyltransferase subunit of acc (ACCD6) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6PK2
Type: protein
Length: 3,376 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propionyl-CoA carboxylase subunit beta
EC: 6.4.1.3
UniProt: A0A0E7XNZ4
Ligands: ORJ
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 43% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Propionyl-CoA carboxylase subunit beta (EC 6.4.1.3)	protein	426	43% helix, 22% strand	A0A0E7XNZ4
B, F	Propionyl-CoA carboxylase subunit beta (EC 6.4.1.3)	protein	424	43% helix, 21% strand	A0A0E7XNZ4
C, G	Propionyl-CoA carboxylase subunit beta (EC 6.4.1.3)	protein	410	41% helix, 22% strand	A0A0E7XNZ4
D, H	Propionyl-CoA carboxylase subunit beta (EC 6.4.1.3)	protein	428	44% helix, 21% strand	A0A0E7XNZ4

Ligands and binding sites

ORJ · 2-{4-[(6-fluoro-1,3-benzothiazol-2-yl)oxy]-2-hydroxyphenyl}-N-methylacetamide · ligand · 8 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	888	0.84	0.85	64	empty
2	1105	0.83	0.84	90	empty
3	857	0.82	0.85	62	empty
4	848	0.81	0.84	65	empty
5	649	0.75	0.81	87	ORJ

Interfaces

15 interfaces between chains.

A–B · 2581 Å² buried · 19 hydrogen bonds · protein-protein
E–F · 2559 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 2349 Å² buried · 15 hydrogen bonds · protein-protein
G–H · 2340 Å² buried · 16 hydrogen bonds · protein-protein
E–H · 572 Å² buried · 1 hydrogen bond · protein-protein

Compared structures

6PK2 · CRYSTAL STRUCTURE OF THE CARBOXYLTRANSFERASE SUBUNIT OF ACC (ACCD6) IN COMPLEX WITH… · the same entry in another collection · chain G against G, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt A0A0E7XNZ4
Elsewhere: RCSB PDB 6PK2 · PDBe 6PK2 · UniProt A0A0E7XNZ4

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