Research workbench
Structure of a quadruplex forming sequence from D. discoideum
Analyse Structure of a quadruplex forming sequence from D. discoideum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6FTU
- Type
- DNA
- Length
- 175 nucleotides
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (26-mer)
- Ligands
- K
- Pockets
- 3 · best druggability 0.65
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, F | DNA (26-mer) | dna | 26 | — | — |
| B | DNA (26-mer) | dna | 25 | — | — |
| D | DNA (26-mer) | dna | 24 | — | — |
| Z | DNA (26-mer) | dna | 22 | — | — |
Ligands and binding sites
- K · Potassium ion · metal · 21 copies · chains A, B, C, D, E, F, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.65 | 0.75 | 46 | empty |
| 2 | 111 | 0.39 | 0.76 | 12 | empty |
| 3 | 54 | 0.23 | 0.72 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–C · 362 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- C–D · 213 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- E–F · 208 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–B · 183 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–E · 32 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 6FTU · Structure of a Quadruplex forming sequence from D. discoideum · 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 6FTU · PDBe 6FTU
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