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Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from methanoculleus marisnigri JR1 at 1.60 a resolution
Analyse Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CMB
- Type
- protein
- Length
- 1,062 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetate decarboxylase
- UniProt
- A3CUL0
- Ligands
- NA, CL
- Pockets
- 10 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 17% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acetoacetate decarboxylase | protein | 265 | 17% helix, 54% strand | A3CUL0 |
| B, C | Acetoacetate decarboxylase | protein | 266 | 17% helix, 54% strand | A3CUL0 |
Ligands and binding sites
- NA · Sodium ion · metal · 12 copies · chains A, D, B, C
- CL · Chloride ion · ion · 4 copies · chains A, C, B, D
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, C, D, B
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains A, B
- PE8 · 3,6,9,12,15,18,21-heptaoxatricosane-1,23-diol · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 583 | 0.85 | 0.90 | 79 | NA, PEG, PE8 |
| 2 | 447 | 0.84 | 0.91 | 68 | P33, NA, CL |
| 3 | 438 | 0.83 | 0.91 | 71 | P33, CL |
| 4 | 975 | 0.83 | 0.84 | 84 | PE8 |
| 5 | 296 | 0.71 | 0.85 | 40 | NA |
Interfaces
6 interfaces between chains.
- B–C · 3399 Ų buried · 40 hydrogen bonds · protein-protein
- A–D · 3223 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 612 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 612 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 3CMB · Crystal structure of acetoacetate decarboxylase (YP_001047042.1) from Methanoculleus… · 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 A3CUL0
- Elsewhere: RCSB PDB 3CMB · PDBe 3CMB · UniProt A3CUL0
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