MolNFT v1 · #153594 · DNA
Crystal structure of a two-quartet DNA mixed-PARALLEL/ANTIPARALLEL G- quadruplex (bru)
6JJE · DNA (5'-D(*GP*GP*CP*(BRU)P*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)…: “Crystal structure of a two-quartet DNA mixed-PARALLEL/ANTIPARALLEL G- quadruplex (bru)”. X-ray diffraction, 3 ligands (NCO, K, NA), 1 pocket (best druggability 0.30).…
- PDB
- 6JJE
- Type
- DNA
- Length
- 28 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*CP*(BRU)P*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)- 3')
- Ligands
- NCO, K, NA
- Pockets
- 1 · best druggability 0.30
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*GP*GP*CP*(BRU)P*CP*GP*GP*CP*GP*GP*CP*GP*GP*A)- 3') | dna | 14 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B
- K · Potassium ion · metal · 3 copies · chains A, B
- NA · Sodium ion · metal · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 70 | 0.30 | 0.74 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 603 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 6JJE · Crystal structure of a two-quartet DNA mixed-parallel/antiparallel G-quadruplex (BrU) · 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 6JJE · PDBe 6JJE
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