Research workbench
Crystal structure of a DNA duplex containing 7,8- DIHYDROPYRIDOL[2,3-D]PYRIMIDIN-2-one
Analyse Crystal structure of a DNA duplex containing 7,8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GJH
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3'
- Ligands
- DAP
- Pockets
- 1 · best druggability 0.23
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(B7C)P*GP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- DAP · 6-amidine-2-(4-amidino-phenyl)indole · ligand · 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.23 | 0.73 | 16 | DAP |
Interfaces
1 interface between chains.
- A–B · 569 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3GJH · Crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one · 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
- Elsewhere: RCSB PDB 3GJH · PDBe 3GJH
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.