Research workbench
Crystal structure of the lgra initiation module in the formylation state
Analyse Crystal structure of the lgra initiation module in the formylation state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ES9
- Type
- protein
- Length
- 1,440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Linear gramicidin synthetase subunit a
- UniProt
- Q70LM7
- Ligands
- PNS
- Pockets
- 13 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Linear gramicidin synthetase subunit a | protein | 759 | 32% helix, 21% strand | Q70LM7 |
| B | Linear gramicidin synthetase subunit a | protein | 681 | 30% helix, 25% strand | Q70LM7 |
Ligands and binding sites
- PNS · 4'-phosphopantetheine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.80 | 0.82 | 87 | empty |
| 2 | 1177 | 0.80 | 0.81 | 104 | PNS |
| 3 | 856 | 0.72 | 0.77 | 72 | empty |
| 4 | 360 | 0.71 | 0.83 | 43 | empty |
| 5 | 435 | 0.57 | 0.74 | 53 | empty |
Interfaces
1 interface between chains.
- A–B · 720 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (phosphopantetheinylation).
Compared structures
- 5ES9 · Crystal structure of the LgrA initiation module in the formylation 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 B against A, TM-score 0.96
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 5ES9 · PDBe 5ES9 · UniProt Q70LM7
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