Research workbench
The structure of transcriptional factor arar from bacteroides thetaiotaomicron vpi in complex with target double strand DNA
Analyse The structure of transcriptional factor arar from bacteroides thetaiotaomicron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DDG
- Type
- protein + DNA
- Length
- 503 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional factor arar; DNA (27-mer)
- UniProt
- Q8AAV8
- Pockets
- 12 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcriptional factor arar | protein | 226 | 33% helix, 29% strand | Q8AAV8 |
| B | Transcriptional factor arar | protein | 223 | 33% helix, 30% strand | Q8AAV8 |
| C | DNA (27-mer) | dna | 27 | — | — |
| D | DNA (27-mer) | dna | 27 | — | — |
Ligands and binding sites
- MLA · Malonic acid · additive · 2 copies · chains A, B
- 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
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 278 | 0.63 | 0.80 | 30 | MLA |
| 2 | 110 | 0.57 | 0.85 | 29 | MLA |
| 3 | 276 | 0.53 | 0.75 | 25 | empty |
| 4 | 116 | 0.38 | 0.75 | 24 | empty |
| 5 | 106 | 0.37 | 0.75 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1572 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1191 Ų buried · 118 hydrogen bonds · nucleic-nucleic
- B–D · 614 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 609 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–C · 507 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 17 modified (engineered).
Compared structures
- 5DDG · The 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 5DDG · PDBe 5DDG · UniProt Q8AAV8
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