MolNFT v1 · #162930 · DNA
L-[RU(TAP)2(DPPZ)]2+ bound to the G-quadruplex forming sequence D(TAGGGTT)
6RNL · DNA (5'-D(*TP*AP*GP*GP*GP*TP*T)-3'): “L-[RU(TAP)2(DPPZ)]2+ bound to the G-quadruplex forming sequence D(TAGGGTT)”. X-ray diffraction, 3 ligands (RKL, K, NA), 2 pockets (best druggability 0.33). MolNFT v1 #162930 on GenesisL1: 3D…
- PDB
- 6RNL
- Type
- DNA
- Length
- 28 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*T)-3')
- Ligands
- RKL, K, NA
- Pockets
- 2 · best druggability 0.33
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(*TP*AP*GP*GP*GP*TP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
- RKL · Ru(tap)2(dppz) complex · ligand · 4 copies · chains A, B, D, C
- K · Potassium ion · metal · 2 copies · chains A, B, C, D
- NA · Sodium ion · metal
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 | 82 | 0.33 | 0.75 | 7 | empty |
| 2 | 55 | 0.26 | 0.74 | 11 | empty |
Interfaces
6 interfaces between chains.
- A–B · 326 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- B–C · 268 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- C–D · 243 Ų buried · 13 hydrogen bonds · nucleic-nucleic
- B–D · 222 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- A–D · 202 Ų buried · 11 hydrogen bonds · nucleic-nucleic
Compared structures
- 6RNL · L-[Ru(TAP)2(dppz)]2+ bound to the G-quadruplex forming sequence d(TAGGGTT) · 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 6RNL · PDBe 6RNL
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