MolNFT v1 · #4369 · protein
Biosynthetic thiolase from zoogloea ramigera in complex with CoA
1DLV: “Biosynthetic thiolase from zoogloea ramigera in complex with CoA”. X-ray diffraction, 2 ligands (COA, SO4), 15 pockets (best druggability 0.80). MolNFT v1 #4369 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1DLV
- Type
- protein
- Length
- 1,556 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Biosynthetic thiolase
- EC
- 2.3.1.9
- UniProt
- P07097
- Ligands
- COA, SO4
- Pockets
- 15 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Biosynthetic thiolase (EC 2.3.1.9) | protein | 389 | 39% helix, 23% strand | P07097 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, C, D, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
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 | 117 | 0.80 | 0.98 | 35 | empty |
| 2 | 123 | 0.79 | 0.98 | 33 | empty |
| 3 | 216 | 0.61 | 0.81 | 39 | COA |
| 4 | 134 | 0.60 | 0.84 | 30 | empty |
| 5 | 125 | 0.59 | 0.84 | 29 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2637 Ų buried · 71 hydrogen bonds · protein-protein
- C–D · 2624 Ų buried · 77 hydrogen bonds · protein-protein
- A–D · 664 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 641 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 298 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 1DLV · Biosynthetic thiolase from zoogloea ramigera in complex with CoA · 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 1DLV · PDBe 1DLV · UniProt P07097
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