MolNFT v1 · #28901 · protein + DNA
The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure of the protein-DNA complex
1YSA · DNA (5'- D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*…: “The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices: crystal structure…”. X-ray diffraction, 2 pockets (best druggability 0.70).…
- PDB
- 1YSA
- Type
- protein + DNA
- Length
- 154 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3'); DNA (5'…
- UniProt
- P03069
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*TP*TP*CP*CP*TP*AP*TP*GP*AP*CP*TP*CP*AP*TP*CP*CP*A P*GP*TP*T)-3') | dna | 20 | — | — |
| B | DNA (5'- D(*AP*AP*AP*CP*TP*GP*GP*AP*TP*GP*AP*GP*TP*CP*AP*TP*A P*GP*GP*A)-3') | dna | 20 | — | — |
| C | Protein (GCN4) | protein | 57 | 88% helix, 0% strand | P03069 |
| D | Protein (GCN4) | protein | 57 | 88% helix, 0% strand | P03069 |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.70 | 0.81 | 34 | empty |
| 2 | 80 | 0.46 | 0.82 | 14 | empty |
Interfaces
6 interfaces between chains.
- C–D · 941 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 829 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–D · 327 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–D · 321 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–C · 306 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 1YSA · The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted alpha helices… · the same entry in another collection · chain A against A, TM-score 1.00
- P03069 · AlphaFold monomer V2.0 prediction for general control transcription factor GCN4 (P03069) · a predicted model of the same protein · chain C against A, TM-score 0.85
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 P03069
- Elsewhere: RCSB PDB 1YSA · PDBe 1YSA · UniProt P03069
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