Research workbench
Alkyldiketide-CoA synthase W332G mutant from evodia rutaecarpa
Analyse Alkyldiketide-CoA synthase W332G mutant from evodia rutaecarpa in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WX7
- 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
- 12 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyldiketide-CoA synthase | protein | 370 | 43% helix, 25% strand | — |
| B, D | Alkyldiketide-CoA synthase | protein | 368 | 41% helix, 25% strand | — |
| C | Alkyldiketide-CoA synthase | protein | 376 | 42% helix, 24% strand | — |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 598 | 0.79 | 0.85 | 55 | COA |
| 2 | 335 | 0.76 | 0.86 | 47 | COA |
| 3 | 302 | 0.75 | 0.87 | 44 | COA |
| 4 | 375 | 0.74 | 0.85 | 47 | COA |
| 5 | 341 | 0.64 | 0.80 | 38 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2454 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 2435 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 398 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 222 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5WX7 · Alkyldiketide-CoA synthase W332G 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 5WX7 · PDBe 5WX7
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