Research workbench
Crystal structure of the DNA-binding domain of AdpA, the global transcriptional factor, in complex with a target DNA
Analyse Crystal structure of the DNA-binding domain of AdpA, the global transcriptional… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W6V
- Type
- protein + DNA
- Length
- 143 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.95
- Source
- Streptomyces griseus; SYNTHETIC CONSTRUCT
- Molecule
- AdpA; DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3'); DNA…
- UniProt
- Q9S166
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 2.95 · 3 distinct chains · 70% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | AdpA | protein | 111 | 70% helix, 0% strand | Q9S166 |
| B | DNA (5'-D(*CP*TP*GP*TP*GP*AP*AP*CP*CP*CP*GP*CP*CP*AP*AP*C)-3') | dna | 16 | — | — |
| C | DNA (5'-D(*AP*GP*GP*TP*TP*GP*GP*CP*GP*GP*GP*TP*TP*CP*AP*C)-3') | dna | 16 | — | — |
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 | 186 | 0.63 | 0.84 | 27 | empty |
| 2 | 61 | 0.31 | 0.76 | 14 | empty |
| 3 | 55 | 0.26 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–C · 628 Ų buried · 67 hydrogen bonds · nucleic-nucleic
- A–C · 466 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–B · 369 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3W6V · Crystal structure of the DNA-binding domain of adpa, the global transcriptional factor… · 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 Q9S166
- Elsewhere: RCSB PDB 3W6V · PDBe 3W6V · UniProt Q9S166
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