Research workbench
Self-assembly of a 3D DNA crystal lattice (4X5 duplex version) containing the J28 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
- 6WRI
- 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*AP*TP*GP*AP*CP*TP*CP*CP*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*AP*TP*GP*AP*CP*TP*CP*CP*AP*CP*TP*CP*A)- 3') | dna | 21 | — | — |
| B | DNA (5'-D(P*AP*GP*TP*CP*A)-3') | dna | 5 | — | — |
| C | DNA (5'-D(*TP*CP*TP*GP*AP*GP*TP*GP*G)-3') | dna | 9 | — | — |
| D | DNA (5'-D(P*TP*GP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- CAC · Cacodylate ion · metal · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
5 interfaces between chains.
- A–C · 333 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–D · 332 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- A–B · 251 Ų buried · 16 hydrogen bonds · nucleic-nucleic
- B–C · 108 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–D · 104 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 6WRI · Self-assembly of a 3D DNA crystal lattice (4x5 duplex version) containing the J28… · 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 6WRI · PDBe 6WRI
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.