Research workbench
Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E/DELH221/S227K mutant
Analyse Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E/DELH221/S227K mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LDV
- 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, SO4, CL, NH4
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 25% 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, 25% strand | P07097 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · 6 copies · chains A, C, D
- NH4 · Ammonium ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 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 | 32 | empty |
| 2 | 73 | 0.74 | 0.98 | 24 | empty |
| 3 | 222 | 0.61 | 0.81 | 38 | COA, NH4 |
| 4 | 234 | 0.57 | 0.78 | 36 | COA, NH4 |
| 5 | 147 | 0.56 | 0.82 | 32 | NH4 |
Interfaces
6 interfaces between chains.
- A–B · 2664 Ų buried · 77 hydrogen bonds · protein-protein
- C–D · 2655 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 708 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 661 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 290 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 7LDV · Zoogloea ramigera biosynthetic thiolase Q183Y/Y218E/delH221/S227K mutant · 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 7LDV · PDBe 7LDV · UniProt P07097
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