MolNFT v1 · #138870 · protein
Alkyldiketide-CoA synthase W332Q mutant from evodia rutaecarpa
5WX6: “Alkyldiketide-CoA synthase W332Q mutant from evodia rutaecarpa”. X-ray diffraction, 2 ligands (COA, SO4), 15 pockets (best druggability 0.78). MolNFT v1 #138870 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5WX6
- Type
- protein
- Length
- 1,482 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyldiketide-CoA synthase
- Ligands
- COA, SO4
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyldiketide-CoA synthase | protein | 363 | 44% helix, 25% strand | — |
| B | Alkyldiketide-CoA synthase | protein | 376 | 42% helix, 24% strand | — |
| C | Alkyldiketide-CoA synthase | protein | 368 | 43% helix, 25% strand | — |
| D | Alkyldiketide-CoA synthase | protein | 375 | 43% helix, 24% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 8 copies · chains A, D, C, 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 85 | SO4 |
| 2 | 339 | 0.71 | 0.83 | 40 | COA |
| 3 | 338 | 0.71 | 0.83 | 50 | COA |
| 4 | 313 | 0.69 | 0.83 | 39 | COA |
| 5 | 263 | 0.65 | 0.82 | 32 | COA |
Interfaces
4 interfaces between chains.
- B–C · 2450 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 2445 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 579 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 64 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5WX6 · Alkyldiketide-CoA synthase W332Q mutant from Evodia rutaecarpa · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 5WX6 · PDBe 5WX6
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