Research workbench
Self-assembly of a 3D DNA crystal lattice (4X6 duplex version) containing the J30 immobile holliday junction
Analyse Self-assembly of a 3D DNA crystal lattice (4X6 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
- 7JOI
- 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*AP*CP*GP*GP*GP*AP*CP*TP*CP*A)- 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*GP*AP*CP*GP*GP*GP*AP*CP*TP*CP*A)- 3') | dna | 21 | — | — |
| B | DNA (5'-D(P*CP*CP*GP*TP*CP*A)-3') | dna | 6 | — | — |
| C | DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*C)-3') | dna | 8 | — | — |
| D | DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- 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 · 337 Ų buried · 39 hydrogen bonds · nucleic-nucleic
- A–B · 294 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–C · 287 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- B–C · 101 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- B–D · 100 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 7JOI · Self-assembly of a 3D DNA crystal lattice (4x6 duplex version) containing the J30… · 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 7JOI · PDBe 7JOI
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