Research workbench
Light-activated ruthenium complex bound to a DNA quadruplex
Analyse Light-activated ruthenium complex bound to a DNA quadruplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LS8
- Type
- DNA
- Length
- 29 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*A)-3')
- Ligands
- QHL, K
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*A)-3') | dna | 7 | — | — |
| D | DNA (5'-D(*TP*AP*GP*GP*GP*TP*TP*A)-3') | dna | 8 | — | — |
Ligands and binding sites
- QHL · Delta-[ru(tap2-dppz-cn]2+ · ligand · 6 copies · chains A, C, D, B
- K · Potassium ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 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 | 0.49 | 0.78 | 13 | empty |
| 2 | 140 | 0.46 | 0.78 | 12 | empty |
Interfaces
6 interfaces between chains.
- A–C · 293 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- B–C · 248 Ų buried · 12 hydrogen bonds · nucleic-nucleic
- B–D · 237 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- A–D · 229 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- A–B · 93 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 5LS8 · Light-activated ruthenium complex bound to a DNA quadruplex · 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 5LS8 · PDBe 5LS8
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