Research workbench
The crystal structure of coptisine bound to DNA D(CGTACG)
Analyse The crystal structure of coptisine bound to DNA D(CGTACG) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D9X
- Type
- DNA
- Length
- 22 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*TP*AP*CP*G)-3')
- Ligands
- KPT, CA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') | dna | 5 | — | — |
| B, D | DNA (5'-D(*CP*GP*TP*AP*CP*G)-3') | dna | 6 | — | — |
Ligands and binding sites
- KPT · 6,7-dihydro[1,3]dioxolo[4,5-g][1,3]dioxolo[7,8]isoquino[3,2-a]isoquinolin-5-ium · ligand · chains C, D
- CA · Calcium ion · metal · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- C–D · 185 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- A–B · 177 Ų buried · 17 hydrogen bonds · nucleic-nucleic
- B–C · 175 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- A–D · 175 Ų buried · 4 hydrogen bonds · nucleic-nucleic
- B–D · 172 Ų buried · 4 hydrogen bonds · nucleic-nucleic
Compared structures
- 4D9X · The crystal structure of Coptisine bound to DNA d(CGTACG) · 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 4D9X · PDBe 4D9X
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.