Research workbench
Crystal structure of dimodular LgrA in a condensation state
Analyse Crystal structure of dimodular LgrA in a condensation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MFZ
- Type
- protein
- Length
- 2,374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 6
- Source
- Brevibacillus parabrevis
- Molecule
- Linear gramicidin synthase subunit A
- UniProt
- Q70LM7
- Ligands
- PNS
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 6 · 2 distinct chains · 31% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linear gramicidin synthase subunit A | protein | 1789 | 31% helix, 21% strand | Q70LM7 |
| B | Linear gramicidin synthase subunit A | protein | 585 | 29% helix, 24% strand | Q70LM7 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.89 | 0.90 | 140 | PNS |
| 2 | 967 | 0.86 | 0.87 | 117 | empty |
| 3 | 860 | 0.80 | 0.83 | 85 | empty |
| 4 | 67 | 0.71 | 0.96 | 17 | empty |
| 5 | 445 | 0.71 | 0.81 | 59 | empty |
Interfaces
1 interface between chains.
- A–B · 513 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (phosphopantetheinylation).
Compared structures
- 6MFZ · Crystal structure of dimodular lgra in a condensation state · the same entry in another collection · chain A against A, TM-score 1.00
- Q70LM7 · AlphaFold monomer V2.0 prediction for linear gramicidin synthase subunit a (Q70LM7) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q70LM7
- Elsewhere: RCSB PDB 6MFZ · PDBe 6MFZ · UniProt Q70LM7
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