MolNFT v1 · #25144 · protein
Crystal structure of a autoinducer-2 synthesis protein
1VGX · S-ribosylhomocysteinase: “Crystal structure of a autoinducer-2 synthesis protein”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.75). MolNFT v1 #25144 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1VGX
- Type
- protein
- Length
- 300 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-ribosylhomocysteinase
- EC
- 3.13.1.-
- UniProt
- Q9RRU8
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-ribosylhomocysteinase (EC 3.13.1.-) | protein | 149 | 32% helix, 22% strand | Q9RRU8 |
| B | S-ribosylhomocysteinase (EC 3.13.1.-) | protein | 151 | 32% helix, 22% strand | Q9RRU8 |
Ligands and binding sites
- 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 | 401 | 0.75 | 0.85 | 35 | ZN |
| 2 | 330 | 0.72 | 0.84 | 39 | ZN |
Interfaces
1 interface between chains.
- A–B · 1841 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (oxidation).
Compared structures
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 1VGX · PDBe 1VGX · UniProt Q9RRU8
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