MolNFT v1 · #169576 · DNA
Self-assembly of a 3D DNA crystal lattice (4X5 junction version) containing the J33 immobile holliday junction
6XGN · DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*TP*G)-3'): “Self-assembly of a 3D DNA crystal lattice (4X5 junction version) containing the J33 immobile holliday junction”. X-ray diffraction, 1 pocket (best druggability 0.26). MolNFT v1…
- PDB
- 6XGN
- Type
- DNA
- Length
- 42 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*TP*G)-3'); DNA…
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*TP*TP*G)-3') | dna | 11 | — | — |
| B | DNA (5'-D(P*AP*CP*AP*GP*CP*AP*CP*TP*CP*A)-3') | dna | 10 | — | — |
| C | DNA (5'-D(P*CP*AP*TP*GP*T)-3') | dna | 5 | — | — |
| D | DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*CP*AP*GP*TP*CP*TP*GP*C)- 3') | dna | 16 | — | — |
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 | 67 | 0.26 | 0.72 | 8 | empty |
Interfaces
5 interfaces between chains.
- A–D · 332 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- B–D · 315 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- C–D · 235 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- B–C · 159 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- A–C · 90 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 6XGN · Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J33… · 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 6XGN · PDBe 6XGN
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