MolNFT v1 · #57099 · DNA
Binding of daunomycin to B-D-glucosylated DNA found in protozoa trypanosoma brucei studied by X-ray crystallograph
308D · DNA (5'-D(*CP*GP*TP*AP*CP*G)-3'): “Binding of daunomycin to B-D-glucosylated DNA found in protozoa trypanosoma brucei studied by X-ray…”. X-ray diffraction, 3 ligands (DM1, BGC, MG). MolNFT v1 #57099 on GenesisL1: 3D structure…
- PDB
- 308D
- Type
- DNA
- Length
- 12 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
- Ligands
- DM1, BGC, MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- DM1 · Daunomycin · ligand · 2 copies · chains A, B
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 294 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 glycan (glycosylation).
Compared structures
- 308D · Binding of daunomycin to B-D-glucosylated DNA found in protozoa trypanosoma brucei… · 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 308D · PDBe 308D
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