Research workbench
Structure of acetone carboxylase purified from xanthobacter autotrophicus
Analyse Structure of acetone carboxylase purified from xanthobacter autotrophicus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5M45
- Type
- protein
- Length
- 6,544 residues
- Chains
- 12
- 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
- AE4, AMP, MG, MN, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Acetone carboxylase alpha subunit (EC 6.4.1.6) | protein | 762 | 36% helix, 19% strand | Q8RM03 |
| B, E, H, K | Acetone carboxylase beta subunit (EC 6.4.1.6) | protein | 709 | 39% helix, 26% strand | Q8RM04 |
| C, F, I, L | Acetone carboxylase gamma subunit (EC 6.4.1.6) | protein | 165 | 28% helix, 24% strand | Q8RM02 |
Ligands and binding sites
- AE4 · 3,6,9,12,15-pentaoxaheptadecan-1-ol · ligand · 4 copies · chains A, D, G, J
- AMP · Adenosine monophosphate · ligand · 4 copies · chains B, E, H, K
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MN · Manganese (II) ion · metal · 4 copies · chains A, D, G, J
- ZN · Zinc ion · metal · 4 copies · chains C, F, I, L
- ACT · Acetate ion · additive · 12 copies · chains A, B, D, E, G, H, J, K
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 | 977 | 0.85 | 0.86 | 101 | MG, ACT |
| 2 | 1004 | 0.84 | 0.85 | 84 | MG, ACT |
| 3 | 747 | 0.84 | 0.88 | 80 | MG, ACT |
| 4 | 241 | 0.84 | 0.96 | 45 | AMP, MG |
| 5 | 245 | 0.84 | 0.96 | 44 | AMP, MG |
Interfaces
20 interfaces between chains.
- J–L · 3966 Ų buried · 50 hydrogen bonds · protein-protein
- A–C · 3954 Ų buried · 49 hydrogen bonds · protein-protein
- D–F · 3938 Ų buried · 52 hydrogen bonds · protein-protein
- G–I · 3905 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 3317 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 5M45 · Structure of Acetone Carboxylase purified from Xanthobacter autotrophicus · the same entry in another collection · chain L against L, 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 Q8RM03
- Every structure of UniProt Q8RM04
- Every structure of UniProt Q8RM02
- Elsewhere: RCSB PDB 5M45 · PDBe 5M45 · UniProt Q8RM03 · UniProt Q8RM04 · UniProt Q8RM02
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