Research workbench
Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the J22 immobile holliday junction
Analyse Self-assembly of a 3D DNA crystal lattice (4X6 junction version) containing the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JH9
- 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*CP*TP*GP*A)-3'); DNA…
- Ligands
- MG
- Pockets
- 1 · best druggability 0.22
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*CP*TP*GP*A)-3') | dna | 12 | — | — |
| B | DNA (5'-D(P*CP*GP*GP*CP*AP*CP*TP*CP*A)-3') | dna | 9 | — | — |
| C | DNA (5'-D(P*TP*CP*AP*CP*CP*G)-3') | dna | 6 | — | — |
| D | DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*GP*GP*TP*CP*TP*GP*C)- 3') | dna | 15 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B, C, D
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 | 51 | 0.22 | 0.72 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–D · 344 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–D · 288 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- C–D · 247 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–C · 149 Ų buried · 13 hydrogen bonds · nucleic-nucleic
- A–C · 127 Ų buried · 9 hydrogen bonds · nucleic-nucleic
Compared structures
- 7JH9 · Self-assembly of a 3D DNA crystal lattice (4x6 junction version) containing the J22… · 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 7JH9 · PDBe 7JH9
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