Research workbench
The regulatory domain of yeie, a sulfite sensing lysr-type transcriptional regulator from cronobacter sakazakii (sulfite-bound form)
Analyse The regulatory domain of yeie, a sulfite sensing lysr-type transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ERP
- Type
- protein
- Length
- 773 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysr family transcriptional regulator
- UniProt
- H9BVC9
- Ligands
- SO3
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Lysr family transcriptional regulator | protein | 196 | 34% helix, 29% strand | H9BVC9 |
| B | Lysr family transcriptional regulator | protein | 199 | 35% helix, 28% strand | H9BVC9 |
| D | Lysr family transcriptional regulator | protein | 182 | 32% helix, 27% strand | H9BVC9 |
Ligands and binding sites
- SO3 · Sulfite ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 406 | 0.62 | 0.77 | 49 | empty |
| 2 | 267 | 0.58 | 0.79 | 33 | empty |
| 3 | 205 | 0.53 | 0.77 | 28 | empty |
| 4 | 152 | 0.48 | 0.77 | 23 | empty |
| 5 | 168 | 0.48 | 0.77 | 42 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1122 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1047 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 296 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7ERP · The regulatory domain of YeiE, a sulfite sensing LysR-type transcriptional regulator from… · 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 H9BVC9
- Elsewhere: RCSB PDB 7ERP · PDBe 7ERP · UniProt H9BVC9
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