MolNFT v1 · #134139 · protein
Mechanism of ATP-dependent acetone carboxylation, acetone carboxylase AMP bound structure
5SVB · Acetone carboxylase alpha subunit: “Mechanism of ATP-dependent acetone carboxylation, acetone carboxylase AMP bound structure”. X-ray diffraction, 4 ligands (AMP, MN, ZN), 20 pockets (best druggability 0.84). MolNFT v1 #134139 on…
- PDB
- 5SVB
- Type
- protein
- Length
- 3,239 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
- AMP, MN, ZN, SO4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetone carboxylase alpha subunit (EC 6.4.1.6) | protein | 746 | 35% helix, 19% strand | Q8RM03 |
| B, E | Acetone carboxylase beta subunit (EC 6.4.1.6) | protein | 707 | 38% helix, 25% strand | Q8RM04 |
| C | Acetone carboxylase gamma subunit (EC 6.4.1.6) | protein | 167 | 27% helix, 25% strand | Q8RM02 |
| D | Acetone carboxylase alpha subunit (EC 6.4.1.6) | protein | 747 | 35% helix, 19% strand | Q8RM03 |
| F | Acetone carboxylase gamma subunit (EC 6.4.1.6) | protein | 165 | 27% helix, 24% strand | Q8RM02 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains B, E
- 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 | 1007 | 0.84 | 0.85 | 103 | empty |
| 2 | 339 | 0.83 | 0.93 | 63 | empty |
| 3 | 327 | 0.83 | 0.93 | 56 | empty |
| 4 | 887 | 0.81 | 0.83 | 86 | empty |
| 5 | 238 | 0.81 | 0.94 | 48 | AMP, SO4 |
Interfaces
7 interfaces between chains.
- D–F · 3861 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 3834 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3154 Ų buried · 53 hydrogen bonds · protein-protein
- D–E · 3138 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 2988 Ų buried · 46 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 94 modified (engineered).
Compared structures
- 5SVB · Mechanism of ATP-Dependent Acetone Carboxylation, Acetone Carboxylase AMP bound structure · the same entry in another collection · chain F against F, 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 1.00
- Q8RM03 · AlphaFold monomer V2.0 prediction for acetone carboxylase alpha subunit (Q8RM03) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q8RM04 · AlphaFold monomer V2.0 prediction for acetone carboxylase beta subunit (Q8RM04) · a predicted model of the same protein · chain E against A, TM-score 0.76
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 5SVB · PDBe 5SVB · UniProt Q8RM03 · UniProt Q8RM04 · UniProt Q8RM02
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