Research workbench
A self-assembling D-form DNA crystal lattice
Analyse A self-assembling D-form DNA crystal lattice in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VY6
- 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*AP*AP*CP*TP*CP*A)- 3'); DNA…
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*AP*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*T)-3') | dna | 8 | — | — |
| D | DNA (5'-D(P*GP*GP*TP*CP*TP*GP*C)-3') | dna | 7 | — | — |
Interfaces
5 interfaces between chains.
- A–D · 344 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- A–B · 290 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- A–C · 280 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- B–C · 109 Ų buried · 6 hydrogen bonds · nucleic-nucleic
- B–D · 97 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 5VY6 · A self-assembling D-form DNA crystal lattice · 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 5VY6 · PDBe 5VY6
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