Research workbench
Crystal structure of a autoinducer-2 synthesis protein with bound selenomethionine
Analyse Crystal structure of a autoinducer-2 synthesis protein with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VJE
- Type
- protein
- Length
- 299 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Autoinducer-2 production protein luxs
- EC
- 3.13.1.-
- UniProt
- Q9RRU8
- Ligands
- MSE, ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Autoinducer-2 production protein luxs (EC 3.13.1.-) | protein | 149 | 34% helix, 22% strand | Q9RRU8 |
| B | Autoinducer-2 production protein luxs (EC 3.13.1.-) | protein | 150 | 35% helix, 22% strand | Q9RRU8 |
Ligands and binding sites
- MSE · Selenomethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.72 | 0.91 | 37 | MSE |
| 2 | 166 | 0.66 | 0.87 | 35 | MSE |
Interfaces
1 interface between chains.
- A–B · 2093 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 1VJE · Crystal structure of a autoinducer-2 synthesis protein with bound selenomethionine · the same entry in another collection · chain A against A, TM-score 1.00
- Q9RRU8 · AlphaFold monomer V2.0 prediction for S-ribosylhomocysteine lyase (Q9RRU8) · a predicted model of the same protein · 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 Q9RRU8
- Elsewhere: RCSB PDB 1VJE · PDBe 1VJE · UniProt Q9RRU8
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