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Crystal structure of acetoacetate decarboxylase (adc) (YP_094708.1) from legionella pneumophila subsp. pneumophila str. philadelphia 1 at 1.60 a resolution
Analyse Crystal structure of acetoacetate decarboxylase (adc) (YP_094708.1) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3C8W
- Type
- protein
- Length
- 998 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetate decarboxylase adc
- EC
- 4.1.1.4
- UniProt
- Q5ZXQ9
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 55% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Acetoacetate decarboxylase adc (EC 4.1.1.4) | protein | 250 | 12% helix, 55% strand | Q5ZXQ9 |
| B, C | Acetoacetate decarboxylase adc (EC 4.1.1.4) | protein | 249 | 12% helix, 55% strand | Q5ZXQ9 |
Ligands and binding sites
- CIT · Citric acid · additive · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 299 | 0.77 | 0.89 | 36 | empty |
| 2 | 316 | 0.77 | 0.88 | 43 | empty |
| 3 | 300 | 0.75 | 0.87 | 37 | empty |
| 4 | 74 | 0.74 | 0.98 | 17 | CIT |
| 5 | 301 | 0.73 | 0.86 | 39 | empty |
Interfaces
5 interfaces between chains.
- A–C · 2938 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 759 Ų buried · 14 hydrogen bonds · protein-protein
- B–D · 733 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 660 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 463 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered, nonstandard).
Compared structures
- 3C8W · Crystal structure of acetoacetate decarboxylase (ADC) (YP_094708.1) from Legionella… · 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 Q5ZXQ9
- Elsewhere: RCSB PDB 3C8W · PDBe 3C8W · UniProt Q5ZXQ9
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