MolNFT v1 · #169992 · DNA
TEL25 hybrid four-quartet G-quadruplex with K+
6XT7 · DNA (25-mer): “TEL25 hybrid four-quartet G-quadruplex with K+”. X-ray diffraction, 3 ligands (SPM, K, MG), 4 pockets (best druggability 0.61). MolNFT v1 #169992 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XT7
- Type
- DNA
- Length
- 100 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (25-mer)
- Ligands
- SPM, K, MG
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (25-mer) | dna | 25 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains B, D
- K · Potassium ion · metal · 12 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 685 | 0.61 | 0.73 | 40 | MG |
| 2 | 133 | 0.36 | 0.73 | 14 | empty |
| 3 | 75 | 0.28 | 0.73 | 9 | empty |
| 4 | 59 | 0.26 | 0.73 | 10 | empty |
Interfaces
5 interfaces between chains.
- B–D · 476 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- A–C · 465 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- A–D · 75 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 70 Ų buried · 1 hydrogen bond · nucleic-nucleic
- A–B · 19 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Compared structures
- 6XT7 · Tel25 Hybrid Four-quartet G-quadruplex with K+ · the same entry in another collection · chain C against C, 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 6XT7 · PDBe 6XT7
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