Research workbench

Propionyl-CoA carboxylase of methylorubrum extorquens with bound CoA

Analyse Propionyl-CoA carboxylase of methylorubrum extorquens with bound CoA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YBP
Type: protein
Length: 4,702 residues
Chains: 12
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Propionyl-CoA carboxylase beta chain; Propionyl-CoA carboxylase alpha subunit
EC: 6.4.1.3
UniProt: C5AP75, C5AWU5
Ligands: COA, BTI
Pockets: 20 · best druggability 0.84

Structure

electron microscopy · 7 distinct chains · 23% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Propionyl-CoA carboxylase beta chain (EC 6.4.1.3)	protein	506	42% helix, 18% strand	C5AP75
G	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	283	16% helix, 32% strand	C5AWU5
H	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	208	14% helix, 40% strand	C5AWU5
I	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	288	17% helix, 31% strand	C5AWU5
J	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	303	17% helix, 30% strand	C5AWU5
K	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	293	19% helix, 31% strand	C5AWU5
L	Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3)	protein	291	18% helix, 33% strand	C5AWU5

Ligands and binding sites

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

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	1040	0.84	0.85	79	empty
2	1024	0.84	0.85	79	empty
3	1025	0.84	0.85	70	empty
4	1149	0.84	0.85	89	empty
5	1187	0.84	0.84	81	empty

Interfaces

33 interfaces between chains.

C–D · 5116 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 5115 Å² buried · 16 hydrogen bonds · protein-protein
A–B · 4995 Å² buried · 19 hydrogen bonds · protein-protein
F–K · 2148 Å² buried · 20 hydrogen bonds · protein-protein
B–J · 2100 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (biotinylation).

Compared structures

6YBP · Propionyl-CoA carboxylase of Methylorubrum extorquens with bound CoA · the same entry in another collection · chain A against A, 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 C5AP75
Every structure of UniProt C5AWU5
Elsewhere: RCSB PDB 6YBP · PDBe 6YBP · UniProt C5AP75 · UniProt C5AWU5

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