Research workbench
Self-assembly of a 3D DNA crystal lattice (4X5 junction version) containing the J23 immobile holliday junction
Analyse Self-assembly of a 3D DNA crystal lattice (4X5 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
- 6XFG
- 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*G)-3'); DNA…
- Ligands
- CAC
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*G)-3') | dna | 11 | — | — |
| B | DNA (5'-D(P*AP*CP*AP*CP*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*GP*GP*GP*TP*CP*TP*GP*C)- 3') | dna | 16 | — | — |
Ligands and binding sites
- CAC · Cacodylate ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–D · 343 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- B–D · 341 Ų buried · 30 hydrogen bonds · nucleic-nucleic
- C–D · 254 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- B–C · 151 Ų buried · 14 hydrogen bonds · nucleic-nucleic
- A–C · 100 Ų buried · 9 hydrogen bonds · nucleic-nucleic
Compared structures
- 6XFG · Self-assembly of a 3D DNA crystal lattice (4x5 junction version) containing the J23… · 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 6XFG · PDBe 6XFG
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