MolNFT v1 · #123539 · protein
Crystal structure of the lgra initiation module excluding the asub domain: F-a-delta-sub
5JNF · Linear gramicidin synthase subunit a: “Crystal structure of the lgra initiation module excluding the asub domain: F-a-delta-sub”. X-ray diffraction, 19 pockets (best druggability 0.78). MolNFT v1 #123539 on GenesisL1: 3D structure…
- PDB
- 5JNF
- Type
- protein
- Length
- 2,329 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linear gramicidin synthase subunit a
- UniProt
- Q70LM7
- Pockets
- 19 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Linear gramicidin synthase subunit a | protein | 583 | 32% helix, 25% strand | Q70LM7 |
| A | Linear gramicidin synthase subunit a | protein | 585 | 31% helix, 25% strand | Q70LM7 |
| B | Linear gramicidin synthase subunit a | protein | 580 | 30% helix, 24% strand | Q70LM7 |
| D | Linear gramicidin synthase subunit a | protein | 581 | 32% helix, 25% strand | Q70LM7 |
Ligands and binding sites
- FMT · Formic acid · additive · 5 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 843 | 0.78 | 0.81 | 82 | FMT |
| 2 | 868 | 0.77 | 0.80 | 74 | FMT |
| 3 | 549 | 0.70 | 0.80 | 58 | empty |
| 4 | 527 | 0.70 | 0.80 | 62 | empty |
| 5 | 286 | 0.68 | 0.83 | 39 | empty |
Interfaces
2 interfaces between chains.
- C–A · 1790 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 243 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5JNF · Crystal structure of the LgrA initiation module excluding the Asub domain: F-A-delta-sub · the same entry in another collection · chain D against D, 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 5JNF · PDBe 5JNF · UniProt Q70LM7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.