MolNFT v1 · #16492 · DNA
Structure of the first parallel DNA quadruplex-drug complex
1O0K · 5'-D(*TP*GP*GP*GP*GP*T)-3': “Structure of the first parallel DNA quadruplex-drug complex”. X-ray diffraction, 2 ligands (DM1, NA). MolNFT v1 #16492 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1O0K
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*GP*GP*GP*GP*T)-3'
- Ligands
- DM1, NA
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 5'-D(*TP*GP*GP*GP*GP*T)-3' | dna | 5 | — | — |
| B | 5'-D(*TP*GP*GP*GP*GP*T)-3' | dna | 4 | — | — |
| C | 5'-D(*TP*GP*GP*GP*GP*T)-3' | dna | 6 | — | — |
Ligands and binding sites
- DM1 · Daunomycin · ligand · 3 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- B–C · 227 Ų buried · 17 hydrogen bonds · nucleic-nucleic
- A–B · 224 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- A–D · 220 Ų buried · 16 hydrogen bonds · nucleic-nucleic
- C–D · 209 Ų buried · 16 hydrogen bonds · nucleic-nucleic
- A–C · 46 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 1O0K · Structure of the First Parallel DNA Quadruplex-drug Complex · 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 1O0K · PDBe 1O0K
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