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The crystal structure of possible transcriptional regulator yydk from bacillus subtilis subsp. subtilis str. 168
Analyse The crystal structure of possible transcriptional regulator yydk from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BWG
- Type
- protein
- Length
- 675 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized hth-type transcriptional regulator yydk
- UniProt
- Q45591
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized hth-type transcriptional regulator yydk | protein | 223 | 27% helix, 36% strand | Q45591 |
| B | Uncharacterized hth-type transcriptional regulator yydk | protein | 228 | 28% helix, 36% strand | Q45591 |
| C | Uncharacterized hth-type transcriptional regulator yydk | protein | 224 | 27% helix, 34% strand | Q45591 |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.74 | 0.92 | 29 | empty |
| 2 | 667 | 0.72 | 0.79 | 62 | empty |
| 3 | 233 | 0.71 | 0.86 | 32 | empty |
| 4 | 295 | 0.68 | 0.83 | 43 | empty |
| 5 | 160 | 0.59 | 0.83 | 30 | EDO |
Interfaces
3 interfaces between chains.
- A–B · 1910 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 350 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 196 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 3BWG · The crystal structure of possible transcriptional regulator YydK from Bacillus subtilis… · the same entry in another collection · chain A against A, TM-score 1.00
- Q45591 · AlphaFold monomer V2.0 prediction for uncharacterized hth-type transcriptional regulator… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q45591
- Elsewhere: RCSB PDB 3BWG · PDBe 3BWG · UniProt Q45591
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