MolNFT v1 · #53111 · protein
Biosynthetic thiolase from Z. ramigera. complex of the N316D mutant with coenzyme a.
2WKV · Acetyl-CoA acetyltransferase: “Biosynthetic thiolase from Z. ramigera. complex of the N316D mutant with coenzyme a.”. X-ray diffraction, 3 ligands (COA, NA, SO4), 15 pockets (best druggability 0.78). MolNFT v1 #53111 on GenesisL1…
- PDB
- 2WKV
- Type
- protein
- Length
- 1,556 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, NA, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 389 | 39% helix, 24% strand | P07097 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, D, B, C
- NA · Sodium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.78 | 0.98 | 33 | empty |
| 2 | 92 | 0.77 | 0.98 | 35 | empty |
| 3 | 228 | 0.64 | 0.82 | 41 | COA |
| 4 | 205 | 0.64 | 0.83 | 44 | COA |
| 5 | 146 | 0.58 | 0.83 | 28 | COA |
Interfaces
6 interfaces between chains.
- A–B · 2637 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 2635 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 704 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 699 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 304 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 2WKV · Biosynthetic thiolase from Z. ramigera. complex of the N316D mutant with coenzyme a. · the same entry in another collection · chain A against A, TM-score 1.00
- P07097 · AlphaFold monomer V2.0 prediction for acetyl-CoA acetyltransferase (P07097) · a predicted model of the same protein · chain A 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 2WKV · PDBe 2WKV · UniProt P07097
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