MolNFT v1 · #117275 · DNA
Crystal structure of 2'-propargyl-modified DNA 8MER-duplex
5E36 · DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3'): “Crystal structure of 2'-propargyl-modified DNA 8MER-duplex”. X-ray diffraction, 1 ligand (MG). MolNFT v1 #117275 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5E36
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3')
- Ligands
- MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA (5'-D(*GP*(OMU)P*GP*TP*(5JO)P*CP*AP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
2 interfaces between chains.
- A–B · 367 Ų buried · 29 hydrogen bonds · nucleic-nucleic
- A–C · 102 Ų buried · 0 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 5E36 · Crystal structure of 2'-propargyl-modified DNA 8mer-duplex · 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 5E36 · PDBe 5E36
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