Research workbench
Crystal structure of the F-a domains of the lgra initiation module soaked with fon, ampcpp, and valine.
Analyse Crystal structure of the F-a domains of the lgra initiation module soaked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ES7
- Type
- protein
- Length
- 580 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linear gramicidin synthetase subunit a
- UniProt
- Q70LM7
- Ligands
- FON, VAL, APC
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linear gramicidin synthetase subunit a | protein | 580 | 32% helix, 24% strand | Q70LM7 |
Ligands and binding sites
- FON · N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid · ligand · chains A
- VAL · Valine · ligand · chains A
- APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 321 | 0.71 | 0.84 | 40 | FON |
| 2 | 357 | 0.60 | 0.77 | 45 | VAL, APC |
| 3 | 110 | 0.44 | 0.78 | 18 | empty |
| 4 | 103 | 0.41 | 0.77 | 19 | empty |
| 5 | 134 | 0.37 | 0.72 | 30 | empty |
Compared structures
- 5ES7 · Crystal structure of the F-A domains of the LgrA initiation module soaked with FON… · 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 5ES7 · PDBe 5ES7 · UniProt Q70LM7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.