Research workbench
SWIT_4259, an acetoacetate decarboxylase-like enzyme from sphingomonas wittichii RW1
Analyse SWIT_4259, an acetoacetate decarboxylase-like enzyme from sphingomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UPB
- Type
- protein
- Length
- 1,021 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetoacetate decarboxylase
- UniProt
- A5VE83
- Pockets
- 12 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Acetoacetate decarboxylase | protein | 256 | 11% helix, 54% strand | A5VE83 |
| C | Acetoacetate decarboxylase | protein | 255 | 11% helix, 54% strand | A5VE83 |
| D | Acetoacetate decarboxylase | protein | 254 | 11% helix, 52% strand | A5VE83 |
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.83 | 0.90 | 61 | empty |
| 2 | 276 | 0.81 | 0.92 | 41 | empty |
| 3 | 597 | 0.80 | 0.86 | 62 | empty |
| 4 | 229 | 0.79 | 0.92 | 43 | empty |
| 5 | 434 | 0.78 | 0.87 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2811 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2753 Ų buried · 42 hydrogen bonds · protein-protein
- B–D · 1827 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1823 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 302 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5UPB · Swit_4259, an Acetoacetate Decarboxylase-like Enzyme from Sphingomonas wittichii RW1 · 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 A5VE83
- Elsewhere: RCSB PDB 5UPB · PDBe 5UPB · UniProt A5VE83
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