Research workbench
Structure of the regulatory domain of the arac family transcriptional activator rhar
Analyse Structure of the regulatory domain of the arac family transcriptional activator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U9E
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth-type transcriptional activator rhar
- UniProt
- C5A074
- Ligands
- RM4, NI
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth-type transcriptional activator rhar | protein | 158 | 29% helix, 37% strand | C5A074 |
| B | Hth-type transcriptional activator rhar | protein | 156 | 29% helix, 37% strand | C5A074 |
Ligands and binding sites
- RM4 · beta-L-rhamnopyranose · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 134 | 0.47 | 0.78 | 29 | empty |
| 2 | 68 | 0.41 | 0.80 | 20 | RM4 |
| 3 | 50 | 0.32 | 0.78 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 898 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5U9E · Structure of the Regulatory Domain of the AraC Family Transcriptional Activator RhaR · the same entry in another collection · chain A against A, TM-score 1.00
- C5A074 · AlphaFold monomer V2.0 prediction for hth-type transcriptional activator rhar (C5A074) · a predicted model of the same protein · chain B 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 C5A074
- Elsewhere: RCSB PDB 5U9E · PDBe 5U9E · UniProt C5A074
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