MolNFT v1 · #64777 · DNA
An inverted anthraquinone-DNA crystal structure
3GDD · 5'-D(*(BRU)P*AP*GP*G)-3': “An inverted anthraquinone-DNA crystal structure”. X-ray diffraction, 2 ligands (5BD, MG). MolNFT v1 #64777 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3GDD
- Type
- DNA
- Length
- 8 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*(BRU)P*AP*GP*G)-3'
- Ligands
- 5BD, MG
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*(BRU)P*AP*GP*G)-3' | dna | 4 | — | — |
Ligands and binding sites
- 5BD · N,N'-(9,10-dioxo-9,10-dihydroanthracene-2,7-diyl)bis[2-(dimethylamino)acetamide] · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 171 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3GDD · An inverted anthraqui -DNA crystal structure · 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 3GDD · PDBe 3GDD
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