Research workbench
Crystal structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with L-arabinose
Analyse Crystal structure of transcriptional factor arar from bacteroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DEQ
- Type
- protein
- Length
- 437 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator arar
- UniProt
- Q8AAV8
- Ligands
- ARA, SO4
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional regulator arar | protein | 214 | 30% helix, 29% strand | Q8AAV8 |
| B | Transcriptional regulator arar | protein | 223 | 28% helix, 28% strand | Q8AAV8 |
Ligands and binding sites
- ARA · alpha-L-arabinopyranose · sugar · 2 copies · chains A, B
- SO4 · Sulfate ion · ion
- FMT · Formic acid · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1062 | 0.75 | 0.77 | 96 | FMT |
| 2 | 111 | 0.38 | 0.74 | 21 | empty |
| 3 | 62 | 0.31 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2027 Ų buried · 25 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 5DEQ · Crystal structure of transcriptional factor AraR from Bacteroides thetaiotaomicron VPI in… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8AAV8
- Elsewhere: RCSB PDB 5DEQ · PDBe 5DEQ · UniProt Q8AAV8
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