Research workbench
Solution structure of the covalent duocarmycin a-DNA duplex complex
Analyse Solution structure of the covalent duocarmycin a-DNA duplex complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 107D
- Type
- DNA
- Length
- 14 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3'); DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3')
- Ligands
- DUO
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*CP*TP*TP*TP*TP*C)-3') | dna | 7 | — | — |
| B | DNA (5'-D(*GP*AP*AP*AP*AP*GP*G)-3') | dna | 7 | — | — |
Ligands and binding sites
- DUO · 4-hydroxy-2,8-dimethyl-1-oxo-6-(4,5,6-trimethoxy-1H-indole-2-carbonyl)-1,2,3,6,7,8-hexahydro-3,6-diaza-as-indacene-2-carboxylic acid methyl ester · ligand · 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 · 305 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 107D · Solution structure of the covalent duocarmycin a-DNA duplex complex · 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 107D · PDBe 107D
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