MolNFT v1 · #141465 · DNA
Solution structure for the unique dimeric 4:2 complex of a PLATINUM(II)-based tripod bound to a hybrid-1 human telomeric G- quadruplex
5Z8F · G-quadruplex DNA (26-mer): “Solution structure for the unique dimeric 4:2 complex of a PLATINUM(II)-based tripod bound to a hybrid-1…”. Solution nmr, 1 ligand (9F0), 4 pockets (best druggability 0.45). MolNFT v1 #141465 on…
- PDB
- 5Z8F
- Type
- DNA
- Length
- 52 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- G-quadruplex DNA (26-mer)
- Ligands
- 9F0
- Pockets
- 4 · best druggability 0.45
Structure
solution nmr · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | G-quadruplex DNA (26-mer) | dna | 26 | — | — |
Ligands and binding sites
- 9F0 · 4-[1-(2,5,8-triazonia-1$L^4-platinabicyclo[3.3.0]octan-1-yl)pyridin-1-ium-4-yl]-N,N-bis[4-[1-(2,5,8-triazonia-1$L^4-platinabicyclo[3.3.0]octan-1-yl) pyridin-1-ium-4-yl]phenyl]aniline · ligand · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 168 | 0.45 | 0.76 | 8 | 9F0 |
| 2 | 141 | 0.41 | 0.75 | 8 | empty |
| 3 | 189 | 0.41 | 0.73 | 12 | empty |
| 4 | 101 | 0.32 | 0.73 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 237 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 5Z8F · Solution structure for the unique dimeric 4:2 complex of a platinum(II)-based tripod… · 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 5Z8F · PDBe 5Z8F
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