Research workbench
Trans-acting transferase from disorazole synthase with malonate
Analyse Trans-acting transferase from disorazole synthase with malonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6APG
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Disd protein
- UniProt
- Q4U443
- Ligands
- CA, SO4
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Disd protein | protein | 281 | 52% helix, 15% strand | Q4U443 |
Ligands and binding sites
- CA · Calcium ion · metal · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.65 | 0.80 | 38 | MLI |
| 2 | 319 | 0.64 | 0.80 | 36 | MLI |
| 3 | 194 | 0.53 | 0.78 | 24 | empty |
| 4 | 101 | 0.43 | 0.78 | 15 | empty |
| 5 | 75 | 0.41 | 0.79 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 590 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6APG · Trans-acting transferase from Disorazole synthase with malonate · 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
- Every structure of UniProt Q4U443
- Elsewhere: RCSB PDB 6APG · PDBe 6APG · UniProt Q4U443
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