MolNFT v2 · #218631 · protein + DNA
Transcription factor BARHL2 homodimer with spacing two bp
8R7F · DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3…: “Transcription factor BARHL2 homodimer with spacing two bp”. X-ray diffraction at 1.98, 4 pockets (best druggability 0.48). MolNFT v2 #218631 on GenesisL1: 3D structure…
- PDB
- 8R7F
- Type
- protein + DNA
- Length
- 159 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.98
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3'); DNA…
- UniProt
- Q9NY43
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · resolution 1.98 · 4 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*CP*TP*AP*AP*AP*CP*GP*GP*GP*CP*AP*AP*TP*TP*AP*G)-3') | dna | 16 | — | — |
| D | DNA (5'-D(*CP*TP*AP*AP*TP*TP*GP*CP*CP*CP*GP*TP*TP*TP*AP*G)-3') | dna | 16 | — | — |
| A | BarH-like 2 homeobox protein | protein | 64 | 69% helix, 0% strand | Q9NY43 |
| E | BarH-like 2 homeobox protein | protein | 63 | 68% helix, 0% strand | Q9NY43 |
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.48 | 0.81 | 20 | empty |
| 2 | 115 | 0.48 | 0.80 | 18 | empty |
| 3 | 134 | 0.45 | 0.77 | 17 | empty |
| 4 | 102 | 0.43 | 0.78 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–D · 702 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- D–E · 591 Ų buried · 16 hydrogen bonds · protein-nucleic
- B–A · 528 Ų buried · 15 hydrogen bonds · protein-nucleic
- D–A · 519 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–E · 518 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- Q9NY43 · AlphaFold monomer V2.0 prediction for barh-like 2 homeobox protein (Q9NY43) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 Q9NY43
- Elsewhere: RCSB PDB 8R7F · PDBe 8R7F · UniProt Q9NY43
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