Research workbench
The crystal structure of a sex pheromone precursor (LMO1757) from listeria monocytogenes egd-E
Analyse The crystal structure of a sex pheromone precursor (LMO1757) from listeria… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HN3
- Type
- protein
- Length
- 1,324 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO1757 protein
- UniProt
- Q8Y6D1
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO1757 protein | protein | 332 | 27% helix, 31% strand | Q8Y6D1 |
| B | LMO1757 protein | protein | 334 | 27% helix, 31% strand | Q8Y6D1 |
| C | LMO1757 protein | protein | 328 | 27% helix, 32% strand | Q8Y6D1 |
| D | LMO1757 protein | protein | 330 | 27% helix, 31% strand | Q8Y6D1 |
Ligands and binding sites
- GOL · Glycerol · additive · 13 copies · chains A, B, D, C
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · chains A, B
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 | 325 | 0.74 | 0.86 | 48 | empty |
| 2 | 56 | 0.71 | 0.98 | 22 | empty |
| 3 | 62 | 0.71 | 0.97 | 13 | empty |
| 4 | 352 | 0.71 | 0.84 | 49 | empty |
| 5 | 1092 | 0.70 | 0.75 | 89 | GOL, PEG |
Interfaces
4 interfaces between chains.
- A–B · 2791 Ų buried · 50 hydrogen bonds · protein-protein
- C–D · 2696 Ų buried · 47 hydrogen bonds · protein-protein
- A–D · 545 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 4HN3 · The crystal structure of a sex pheromone precursor (lmo1757) from Listeria monocytogenes… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8Y6D1
- Elsewhere: RCSB PDB 4HN3 · PDBe 4HN3 · UniProt Q8Y6D1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.