Research workbench
Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain srfte
Analyse Structural basis for the cyclization of the lipopeptide antibiotic surfactin by… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JMK
- Type
- protein
- Length
- 452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surfactin synthetase
- UniProt
- Q08787
- Ligands
- SO4
- Pockets
- 5 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Surfactin synthetase | protein | 222 | 40% helix, 21% strand | Q08787 |
| O | Surfactin synthetase | protein | 230 | 39% helix, 20% strand | Q08787 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains C, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 647 | 0.70 | 0.78 | 79 | empty |
| 2 | 78 | 0.49 | 0.83 | 20 | empty |
| 3 | 81 | 0.46 | 0.82 | 19 | empty |
| 4 | 67 | 0.44 | 0.82 | 18 | empty |
| 5 | 83 | 0.41 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- C–O · 674 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 1JMK · Structural Basis for the Cyclization of the Lipopeptide Antibiotic Surfactin by the… · the same entry in another collection · chain C against C, TM-score 1.00
- Q08787 · AlphaFold monomer V2.0 prediction for surfactin synthase subunit 3 (Q08787) · a predicted model of the same protein · chain O against A, TM-score 0.98
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 Q08787
- Elsewhere: RCSB PDB 1JMK · PDBe 1JMK · UniProt Q08787
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.