MolNFT v1 · #137752 · DNA
A self-assembling L-form DNA crystal lattice
5VY7 · DNA (5'- D(*GP*AP*GP*CP*AP*GP*AP*CP*CP*TP*GP*AP*CP*GP*GP*AP*…: “A self-assembling L-form DNA crystal lattice”. X-ray diffraction. MolNFT v1 #137752 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5VY7
- 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 · 341 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- A–B · 298 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–C · 278 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- B–C · 109 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- B–D · 103 Ų buried · 5 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 42 modified (nucleotide modification).
Compared structures
- 5VY7 · A self-assembling L-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 5VY7 · PDBe 5VY7
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