Research workbench
A novel end-to-end binding of two netropsins to the DNA decamer D(CCCCCIIIII)2
Analyse A novel end-to-end binding of two netropsins to the DNA decamer D(CCCCCIIIII)2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 474D
- Type
- DNA
- Length
- 40 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3')
- Ligands
- NT
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(*CP*CP*CP*(CBR)P*CP*IP*IP*IP*IP*I)-3') | dna | 10 | — | — |
Ligands and binding sites
- NT · Netropsin · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
3 interfaces between chains.
- C–D · 423 Ų buried · 45 hydrogen bonds · nucleic-nucleic
- A–B · 418 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–C · 71 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 474D · A novel end-to-end binding of two netropsins to the DNA decamer D(CCCCCIIIII)2 · the same entry in another collection · chain B against B, 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 474D · PDBe 474D
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