Research workbench
Crystal structure of a 4-domain construct of a mutant of LgrA in the substrate donation state
Analyse Crystal structure of a 4-domain construct of a mutant of LgrA in the substrate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MFX
- Type
- protein
- Length
- 1,186 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Brevibacillus parabrevis
- Molecule
- Linear gramicidin synthase subunit A
- UniProt
- Q70LM7
- Ligands
- 9EF, APC, VAL
- Pockets
- 9 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.2 · 1 distinct chain · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linear gramicidin synthase subunit A | protein | 1186 | 34% helix, 23% strand | Q70LM7 |
Ligands and binding sites
- 9EF · N-[2-(acetylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · chains A
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
- VAL · Valine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.88 | 0.89 | 126 | 9EF |
| 2 | 876 | 0.78 | 0.81 | 87 | APC, VAL |
| 3 | 722 | 0.77 | 0.82 | 75 | empty |
| 4 | 195 | 0.68 | 0.86 | 27 | empty |
| 5 | 65 | 0.54 | 0.87 | 23 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6MFX · Crystal structure of a 4-domain construct of a mutant of lgra in the substrate donation… · 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 0.98
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 Q70LM7
- Elsewhere: RCSB PDB 6MFX · PDBe 6MFX · UniProt Q70LM7
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