Research workbench
Crystal structure of yfir, a putative transcriptional regulator from bacillus subtilis
Analyse Crystal structure of yfir, a putative transcriptional regulator from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RKT
- Type
- protein
- Length
- 404 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein yfir
- UniProt
- O31560
- Ligands
- UNX
- Pockets
- 3 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein yfir | protein | 204 | 77% helix, 0% strand | O31560 |
| B | Protein yfir | protein | 200 | 80% helix, 0% strand | O31560 |
Ligands and binding sites
- UNX · Unknown atom or ion · ion · 39 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.86 | 0.86 | 77 | UNX |
| 2 | 175 | 0.47 | 0.76 | 25 | empty |
| 3 | 60 | 0.29 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1873 Ų buried · 32 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 1RKT · Crystal structure of yfiR, a putative transcriptional regulator from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
- O31560 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 O31560
- Elsewhere: RCSB PDB 1RKT · PDBe 1RKT · UniProt O31560
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.