MolNFT v1 · #134140 · protein
Mechanism of ATP-dependent acetone carboxylation, acetone carboxylase nucleotide-free structure
5SVC · Acetone carboxylase alpha subunit: “Mechanism of ATP-dependent acetone carboxylation, acetone carboxylase nucleotide-free structure”. X-ray diffraction, 3 ligands (MN, ZN, SO4), 20 pockets (best druggability 0.83). MolNFT v1 #134140…
- PDB
- 5SVC
- Type
- protein
- Length
- 3,278 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetone carboxylase alpha subunit; Acetone carboxylase beta subunit; Acetone carboxylase…
- EC
- 6.4.1.6
- UniProt
- Q8RM03, Q8RM04, Q8RM02
- Ligands
- MN, ZN, SO4
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acetone carboxylase alpha subunit (EC 6.4.1.6) | protein | 763 | 36% helix, 19% strand | Q8RM03 |
| B, E | Acetone carboxylase beta subunit (EC 6.4.1.6) | protein | 710 | 37% helix, 25% strand | Q8RM04 |
| C, F | Acetone carboxylase gamma subunit (EC 6.4.1.6) | protein | 166 | 26% helix, 25% strand | Q8RM02 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 2 copies · chains A, D
- ZN · Zinc ion · metal · 2 copies · chains C, F
- SO4 · Sulfate ion · ion · 2 copies · chains B, E
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 | 513 | 0.83 | 0.89 | 81 | SO4 |
| 2 | 486 | 0.83 | 0.90 | 78 | SO4 |
| 3 | 119 | 0.79 | 0.98 | 28 | empty |
| 4 | 79 | 0.76 | 0.98 | 23 | empty |
| 5 | 76 | 0.76 | 0.99 | 21 | empty |
Interfaces
9 interfaces between chains.
- A–C · 3924 Ų buried · 53 hydrogen bonds · protein-protein
- D–F · 3916 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 3212 Ų buried · 55 hydrogen bonds · protein-protein
- D–E · 3068 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3067 Ų buried · 56 hydrogen bonds · protein-protein
Compared structures
- Q8RM03 · AlphaFold monomer V2.0 prediction for acetone carboxylase alpha subunit (Q8RM03) · a predicted model of the same protein · chain D against A, TM-score 1.00
- Q8RM02 · AlphaFold monomer V2.0 prediction for acetone carboxylase gamma subunit (Q8RM02) · a predicted model of the same protein · chain F against A, TM-score 0.99
- Q8RM04 · AlphaFold monomer V2.0 prediction for acetone carboxylase beta subunit (Q8RM04) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q8RM03
- Every structure of UniProt Q8RM04
- Every structure of UniProt Q8RM02
- Elsewhere: RCSB PDB 5SVC · PDBe 5SVC · UniProt Q8RM03 · UniProt Q8RM04 · UniProt Q8RM02
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