MolNFT v1 · #180854 · protein
Zoogloea ramigera biosynthetic thiolase Q183Y mutant, rbcl soak
7LD2 · Acetyl-CoA acetyltransferase: “Zoogloea ramigera biosynthetic thiolase Q183Y mutant, rbcl soak”. X-ray diffraction, 4 ligands (COA, RB, CL), 16 pockets (best druggability 0.79). MolNFT v1 #180854 on GenesisL1: 3D structure, binding…
- PDB
- 7LD2
- 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, RB, CL, SO4
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Acetyl-CoA acetyltransferase (EC 2.3.1.9) | protein | 390 | 38% helix, 24% strand | P07097 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, D, B, C
- RB · Rubidium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 10 copies · chains A, 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
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 118 | 0.79 | 0.98 | 38 | empty |
| 2 | 65 | 0.74 | 0.99 | 25 | empty |
| 3 | 222 | 0.60 | 0.80 | 40 | COA |
| 4 | 137 | 0.59 | 0.84 | 26 | empty |
| 5 | 130 | 0.57 | 0.83 | 25 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2678 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 2657 Ų buried · 73 hydrogen bonds · protein-protein
- B–C · 683 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 660 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 7LD2 · Zoogloea ramigera biosynthetic thiolase Q183Y mutant, RbCl soak · 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 7LD2 · PDBe 7LD2 · UniProt P07097
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