MolNFT v1 · #170570 · protein
Engineered glycolyl-CoA carboxylase (quintuple mutant) with bound CoA
6YBQ · Propionyl-CoA carboxylase beta chain: “Engineered glycolyl-CoA carboxylase (quintuple mutant) with bound CoA”. Electron microscopy, 2 ligands (COA, BTI), 20 pockets (best druggability 0.85). MolNFT v1 #170570 on GenesisL1: 3D…
- PDB
- 6YBQ
- Type
- protein
- Length
- 4,289 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 0.85
Structure
electron microscopy · 5 distinct chains · 26% helix, 33% 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 | 43% helix, 18% strand | C5AP75 |
| G | Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3) | protein | 208 | 14% helix, 41% strand | C5AWU5 |
| H, J, L | Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3) | protein | 210 | 15% helix, 41% strand | C5AWU5 |
| I | Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3) | protein | 206 | 15% helix, 43% strand | C5AWU5 |
| K | Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3) | protein | 209 | 15% helix, 43% 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.85 | 0.86 | 78 | empty |
| 2 | 1137 | 0.84 | 0.85 | 88 | empty |
| 3 | 1161 | 0.84 | 0.85 | 101 | empty |
| 4 | 985 | 0.84 | 0.85 | 71 | empty |
| 5 | 1016 | 0.84 | 0.85 | 71 | empty |
Interfaces
33 interfaces between chains.
- A–B · 5046 Ų buried · 57 hydrogen bonds · protein-protein
- C–D · 5045 Ų buried · 53 hydrogen bonds · protein-protein
- E–F · 5035 Ų buried · 54 hydrogen bonds · protein-protein
- E–I · 1841 Ų buried · 20 hydrogen bonds · protein-protein
- F–K · 1826 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (biotinylation).
Compared structures
- 6YBQ · Engineered glycolyl-CoA carboxylase (quintuple mutant) 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 6YBQ · PDBe 6YBQ · UniProt C5AP75 · UniProt C5AWU5
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