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Crystal structure of a complex between the marine anticancer drug variolin B and DNA
Analyse Crystal structure of a complex between the marine anticancer drug variolin B… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MNB
- Type
- DNA
- Length
- 11 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*TP*AP*CP*G)-3'
- Ligands
- NCO, VAR, CO, NA
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*GP*TP*AP*CP*G)-3' | dna | 5 | — | — |
| B | 5'-D(*CP*GP*TP*AP*CP*G)-3' | dna | 6 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 3 copies · chains A, B
- VAR · 9-amino-5-(2-aminopyrimidin-4-yl)pyrido[3',2':4,5]pyrrolo[1,2-c]pyrimidin-4-ol · ligand · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal · chains A
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 178 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Compared structures
- 4MNB · Crystal Structure of a complex between the marine anticancer drug Variolin B and DNA · 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 4MNB · PDBe 4MNB
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