MolNFT v1 · #11433 · protein
Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain srfte
1JMK · Surfactin synthetase: “Structural basis for the cyclization of the lipopeptide antibiotic surfactin by the thioesterase domain srfte”. X-ray diffraction, 1 ligand (SO4), 5 pockets (best druggability 0.70). MolNFT v1 #11433 on…
- 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
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