MolNFT v2 · #216881 · protein
Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA
8PN7 · Propionyl-CoA carboxylase beta chain: “Engineered glycolyl-CoA carboxylase (G20R variant) with bound CoA”. Electron microscopy at 2.03, 2 ligands (COA, BTI), 20 pockets (best druggability 0.85). MolNFT v2 #216881 on GenesisL1: 3D…
- PDB
- 8PN7
- Type
- protein
- Length
- 4,308 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.03
- Source
- Methylorubrum extorquens AM1
- 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 · resolution 2.03 · 2 distinct chains · 35% helix, 26% 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, 19% strand | C5AP75 |
| G, H, I, J, K, L | Propionyl-CoA carboxylase alpha subunit (EC 6.4.1.3) | protein | 212 | 14% helix, 42% 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 | 1004 | 0.85 | 0.86 | 90 | empty |
| 2 | 1029 | 0.84 | 0.85 | 92 | empty |
| 3 | 1052 | 0.84 | 0.85 | 100 | empty |
| 4 | 840 | 0.84 | 0.86 | 70 | empty |
| 5 | 1067 | 0.84 | 0.85 | 93 | empty |
Interfaces
30 interfaces between chains.
- C–D · 4996 Ų buried · 62 hydrogen bonds · protein-protein
- E–F · 4974 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 4964 Ų buried · 62 hydrogen bonds · protein-protein
- D–L · 1849 Ų buried · 22 hydrogen bonds · protein-protein
- B–J · 1849 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 cofactor (biotinylation).
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 8PN7 · PDBe 8PN7 · UniProt C5AP75 · UniProt C5AWU5
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