Research workbench
The crystal structure of chelerythrine bound to DNA D(CGTACG)
Analyse The crystal structure of chelerythrine 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
- 4D9Y
- 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
- CTI, 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
- CTI · 1,2-dimethoxy-12-methyl[1,3]benzodioxolo[5,6-c]phenanthridin-12-ium · ligand · chains A, B
- 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.
- A–D · 198 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- B–C · 188 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- C–D · 182 Ų buried · 16 hydrogen bonds · nucleic-nucleic
- A–B · 178 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- B–D · 174 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 4D9Y · The crystal structure of Chelerythrine 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 4D9Y · PDBe 4D9Y
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