Research workbench
Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version) containing the J5 immobile holliday junction with R3 symmetry
Analyse Self-assembly of a 3D DNA crystal lattice (4X6 scramble duplex version)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JKH
- Type
- DNA
- Length
- 42 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*CP*CP*GP*TP*CP*G)-3'); DNA (5'- D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*CP*GP*AP*CP*GP*G…
- Ligands
- CAC
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(P*CP*CP*GP*TP*CP*G)-3') | dna | 6 | — | — |
| B | DNA (5'- D(*GP*AP*AP*CP*GP*AP*CP*AP*CP*CP*GP*AP*CP*GP*GP*GP*GP*AP*CP*TP*C)- 3') | dna | 21 | — | — |
| C | DNA (5'-D(*TP*CP*GP*AP*GP*TP*CP*C)-3') | dna | 8 | — | — |
| D | DNA (5'-D(P*GP*TP*GP*TP*CP*GP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
- CAC · Cacodylate ion · metal · 2 copies · chains A, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- B–D · 346 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–B · 299 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- B–C · 269 Ų buried · 28 hydrogen bonds · nucleic-nucleic
- A–D · 106 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–C · 89 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 7JKH · Self-assembly of a 3D DNA crystal lattice (4x6 scramble duplex version) containing the J5… · 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 7JKH · PDBe 7JKH
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