Research workbench
Crystal structure of a rationally designed six-fold symmetric DNA scaffold
Analyse Crystal structure of a rationally designed six-fold symmetric DNA scaffold in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DKL
- Type
- DNA
- Length
- 42 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3'); DNA…
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(P*GP*GP*AP*TP*GP*CP*AP*CP*A)-3') | dna | 9 | — | — |
| B | DNA (5'-D(P*CP*AP*CP*AP*CP*CP*GP*TP*AP*C)-3') | dna | 10 | — | — |
| C | DNA (5'-D(P*TP*GP*TP*GP*CP*TP*GP*TP*GP*CP*T)-3') | dna | 11 | — | — |
| D | DNA (5'-D(P*GP*TP*AP*CP*GP*GP*AP*TP*CP*CP*AP*G)-3') | dna | 12 | — | — |
Interfaces
5 interfaces between chains.
- B–D · 268 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- C–D · 234 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- A–C · 233 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- A–D · 222 Ų buried · 22 hydrogen bonds · nucleic-nucleic
- B–C · 205 Ų buried · 20 hydrogen bonds · nucleic-nucleic
Compared structures
- 6DKL · Crystal Structure of a Rationally Designed Six-Fold Symmetric DNA Scaffold · 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 6DKL · PDBe 6DKL
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