Research workbench
Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH 9.5
Analyse Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NL7
- Type
- protein
- Length
- 1,560 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 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 390 | 39% helix, 23% 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
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 | 104 | 0.78 | 0.98 | 35 | empty |
| 2 | 65 | 0.73 | 0.98 | 24 | empty |
| 3 | 131 | 0.55 | 0.82 | 24 | empty |
| 4 | 114 | 0.54 | 0.82 | 23 | empty |
| 5 | 146 | 0.54 | 0.80 | 25 | COA |
Interfaces
6 interfaces between chains.
- A–B · 2660 Ų buried · 78 hydrogen bonds · protein-protein
- C–D · 2636 Ų buried · 78 hydrogen bonds · protein-protein
- B–C · 680 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 673 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 1NL7 · Z. ramigera biosynthetic thiolase, acetylated enzyme complexed with CoA at pH 9.5 · 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 1NL7 · PDBe 1NL7 · UniProt P07097
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