Research workbench
The three-dimensional structure of trmb, a global transcriptional regulator of the hyperthermophilic archaeon pyrococcus furiosus in complex with sucrose
Analyse The three-dimensional structure of trmb, a global transcriptional regulator of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QPH
- Type
- protein
- Length
- 335 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trmb, a global transcription regulator
- UniProt
- Q9HGZ9
- Ligands
- GLC, FRU
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trmb, a global transcription regulator | protein | 335 | 33% helix, 30% strand | Q9HGZ9 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · chains A
- FRU · beta-D-fructofuranose · sugar · chains A
- GOL · Glycerol · additive · 9 copies · chains A
- ACT · Acetate ion · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.56 | 0.81 | 27 | empty |
| 2 | 150 | 0.52 | 0.79 | 22 | GLC, FRU |
| 3 | 266 | 0.49 | 0.73 | 34 | GOL |
| 4 | 53 | 0.46 | 0.85 | 16 | empty |
| 5 | 51 | 0.31 | 0.77 | 16 | empty |
Compared structures
- 3QPH · The three-dimensional structure of TrmB, a global transcriptional regulator of the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9HGZ9 · AlphaFold monomer V2.0 prediction for hth-type sugar sensing transcriptional regulator… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9HGZ9
- Elsewhere: RCSB PDB 3QPH · PDBe 3QPH · UniProt Q9HGZ9
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