Research workbench
Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J6 immobile Holliday junction
Analyse Self-assembly of a 3D DNA crystal lattice (4x5 duplex 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
- 6X8B
- Type
- DNA
- Length
- 42 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.899
- Molecule
- DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*AP*AP*GP*AP*CP*TP*TP*CP*AP*CP*TP*CP*A)-3'); DNA…
- Ligands
- MG, CAC
Structure
x-ray diffraction · resolution 2.899 · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*GP*AP*GP*CP*AP*GP*AP*CP*AP*AP*GP*AP*CP*TP*TP*CP*AP*CP*TP*CP*A)-3') | dna | 21 | — | — |
| B | DNA (5'-D(P*AP*GP*TP*CP*T)-3') | dna | 5 | — | — |
| C | DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*A)-3') | dna | 9 | — | — |
| D | DNA (5'-D(P*TP*GP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, D, B, C
- CAC · Cacodylate ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–D · 341 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- A–C · 334 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- A–B · 244 Ų buried · 15 hydrogen bonds · nucleic-nucleic
- B–D · 102 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 98 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 6X8B · Self-assembly of a 3D DNA crystal lattice (4X5 duplex version) containing the J6 immobile… · 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 6X8B · PDBe 6X8B
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