Research workbench
Structure of the effector-binding domain of arabinose repressor arar from bacillus subtilis
Analyse Structure of the effector-binding domain of arabinose repressor arar from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3TB6
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arabinose metabolism transcriptional repressor
- UniProt
- P96711
- Ligands
- ARB
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arabinose metabolism transcriptional repressor | protein | 283 | 41% helix, 18% strand | P96711 |
| B | Arabinose metabolism transcriptional repressor | protein | 283 | 42% helix, 18% strand | P96711 |
Ligands and binding sites
- ARB · beta-L-arabinopyranose · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 159 | 0.72 | 0.90 | 31 | ARB |
| 2 | 219 | 0.68 | 0.85 | 35 | ARB |
| 3 | 60 | 0.51 | 0.87 | 16 | empty |
| 4 | 58 | 0.50 | 0.86 | 16 | empty |
| 5 | 170 | 0.45 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 983 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3TB6 · Structure of the effector-binding domain of arabinose repressor AraR from Bacillus… · the same entry in another collection · chain A against A, TM-score 1.00
- P96711 · AlphaFold monomer V2.0 prediction for arabinose metabolism transcriptional repressor… · a predicted model of the same protein · chain A 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 P96711
- Elsewhere: RCSB PDB 3TB6 · PDBe 3TB6 · UniProt P96711
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