MolNFT v1 · #117373 · protein
High resolution crystal structure of luxs - quorum sensor molecular complex from salmonella typhi at 1.58 ångströms
5E68 · S-ribosylhomocysteine lyase: “High resolution crystal structure of luxs - quorum sensor molecular complex from salmonella typhi at 1.58…”. X-ray diffraction, 3 ligands (PAV, MET, ZN), 2 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 5E68
- Type
- protein
- Length
- 339 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-ribosylhomocysteine lyase
- EC
- 4.4.1.21
- UniProt
- Q8Z4D7
- Ligands
- PAV, MET, ZN
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-ribosylhomocysteine lyase (EC 4.4.1.21) | protein | 167 | 37% helix, 21% strand | Q8Z4D7 |
| B | S-ribosylhomocysteine lyase (EC 4.4.1.21) | protein | 172 | 36% helix, 22% strand | Q8Z4D7 |
Ligands and binding sites
- PAV · (2R,4S)-2-methyl-2,3,3,4-tetrahydroxytetrahydrofuran · ligand · chains A, B
- MET · Methionine · ligand · 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 | 361 | 0.72 | 0.84 | 33 | empty |
| 2 | 180 | 0.68 | 0.87 | 33 | MET |
Interfaces
1 interface between chains.
- A–B · 2313 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
- 5E68 · High resolution crystal structure of LuxS - Quorum sensor molecular complex from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8Z4D7 · AlphaFold monomer V2.0 prediction for S-ribosylhomocysteine lyase (Q8Z4D7) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q8Z4D7
- Elsewhere: RCSB PDB 5E68 · PDBe 5E68 · UniProt Q8Z4D7
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