MolNFT v1 · #147832 · protein
Lar controls the expression of the listeria monocytogenes agr system and mediates virulence.
6EP3 · LMO0651 protein: “Lar controls the expression of the listeria monocytogenes agr system and mediates virulence.”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.77). MolNFT v1 #147832 on GenesisL1: 3D structure…
- PDB
- 6EP3
- Type
- protein
- Length
- 433 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LMO0651 protein
- UniProt
- Q8Y982
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 74% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LMO0651 protein | protein | 215 | 73% helix, 2% strand | Q8Y982 |
| B | LMO0651 protein | protein | 218 | 74% helix, 4% strand | Q8Y982 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.77 | 0.79 | 74 | empty |
| 2 | 462 | 0.60 | 0.75 | 45 | EDO |
| 3 | 52 | 0.38 | 0.81 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1160 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6EP3 · Lar controls the expression of the Listeria monocytogenes agr system and mediates… · 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 Q8Y982
- Elsewhere: RCSB PDB 6EP3 · PDBe 6EP3 · UniProt Q8Y982
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