Research workbench
DNA recognition by GAL4: structure of a PROTEIN/DNA complex
Analyse DNA recognition by GAL4: structure of a PROTEIN/DNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1D66
- Type
- protein + DNA
- Length
- 152 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3'); DNA (5'…
- UniProt
- P04386
- Ligands
- CD
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | DNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*AP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3') | dna | 19 | — | — |
| E | DNA (5'- D(*CP*CP*GP*GP*AP*GP*GP*AP*CP*TP*GP*TP*CP*CP*TP*CP*C P*GP*G)-3') | dna | 19 | — | — |
| A, B | Protein (GAL4) | protein | 57 | 40% helix, 0% strand | P04386 |
Ligands and binding sites
- CD · Cadmium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 327 | 0.58 | 0.78 | 39 | empty |
Interfaces
6 interfaces between chains.
- D–E · 867 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- A–B · 660 Ų buried · 7 hydrogen bonds · protein-protein
- E–A · 485 Ų buried · 6 hydrogen bonds · protein-nucleic
- D–B · 449 Ų buried · 8 hydrogen bonds · protein-nucleic
- D–A · 275 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
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 P04386
- Elsewhere: RCSB PDB 1D66 · PDBe 1D66 · UniProt P04386
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