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Biosynthetic thiolase from Z. ramigera. complex of the oxidised enzyme with coenzyme a.
Analyse Biosynthetic thiolase from Z. ramigera. complex of the oxidised enzyme with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VU0
- Type
- protein
- Length
- 1,563 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetyl-CoA acetyltransferase
- EC
- 2.3.1.9
- UniProt
- P07097
- Ligands
- COA, SO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 391 | 39% helix, 23% strand | P07097 |
| D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 390 | 39% helix, 24% strand | P07097 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 2 copies · chains A, C, D, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.79 | 0.98 | 41 | empty |
| 2 | 64 | 0.73 | 0.99 | 20 | empty |
| 3 | 139 | 0.59 | 0.83 | 29 | empty |
| 4 | 127 | 0.56 | 0.82 | 28 | empty |
| 5 | 123 | 0.55 | 0.82 | 23 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2650 Ų buried · 75 hydrogen bonds · protein-protein
- C–D · 2642 Ų buried · 76 hydrogen bonds · protein-protein
- B–C · 713 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 654 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 314 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 2VU0 · Biosynthetic thiolase from Z. ramigera. Complex of the oxidised enzyme with coenzyme A. · the same entry in another collection · chain B against B, TM-score 1.00
- P07097 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P07097) · a predicted model of the same protein · chain D against A, TM-score 0.99
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 P07097
- Elsewhere: RCSB PDB 2VU0 · PDBe 2VU0 · UniProt P07097
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