MolNFT v1 · #72380 · protein

Crystal structure of the holoenzyme of propionyl-CoA carboxylase (pcc)

3N6R · Propionyl-CoA carboxylase, alpha subunit: “Crystal structure of the holoenzyme of propionyl-CoA carboxylase (pcc)”. X-ray diffraction, 1 ligand (BTI), 20 pockets (best druggability 0.84). MolNFT v1 #72380 on GenesisL1: 3D structure…

PDB: 3N6R
Type: protein
Length: 6,747 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propionyl-CoA carboxylase, alpha subunit; Propionyl-CoA carboxylase, beta subunit
EC: 6.4.1.3
UniProt: Q5LUF3, Q168G2
Ligands: BTI
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Propionyl-CoA carboxylase, alpha subunit (EC 6.4.1.3)	protein	591	26% helix, 27% strand	Q5LUF3
B, D, F, H, J, L	Propionyl-CoA carboxylase, beta subunit (EC 6.4.1.3)	protein	506	42% helix, 18% strand	Q168G2
G, I, K	Propionyl-CoA carboxylase, alpha subunit (EC 6.4.1.3)	protein	646	27% helix, 27% strand	Q5LUF3

Ligands and binding sites

BTI · 5-(hexahydro-2-oxo-1H-thieno[3,4-d]imidazol-6-yl) pentanal · ligand · 6 copies · chains A, B, J, C, D, L, E, F, H, G, I, K

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1188	0.84	0.85	118	empty
2	766	0.84	0.87	72	empty
3	746	0.84	0.88	83	empty
4	982	0.82	0.84	108	empty
5	1028	0.81	0.82	97	empty

Interfaces

30 interfaces between chains.

D–L · 5107 Å² buried · 59 hydrogen bonds · protein-protein
F–H · 5107 Å² buried · 61 hydrogen bonds · protein-protein
B–J · 5096 Å² buried · 69 hydrogen bonds · protein-protein
A–B · 2083 Å² buried · 33 hydrogen bonds · protein-protein
K–L · 2076 Å² buried · 29 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (biotinylation).

Compared structures

3N6R · CRYSTAL STRUCTURE OF the holoenzyme of PROPIONYL-COA CARBOXYLASE (PCC) · the same entry in another collection · chain L against L, 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 Q5LUF3
Every structure of UniProt Q168G2
Elsewhere: RCSB PDB 3N6R · PDBe 3N6R · UniProt Q5LUF3 · UniProt Q168G2

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