Research workbench
Solution structure of the complex formed between a left-handed wedge- shaped spirocyclic molecule and bulged DNA
Analyse Solution structure of the complex formed between a left-handed wedge- shaped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1R4E
- Type
- DNA
- Length
- 26 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3'…
- Ligands
- DDI
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*AP*CP*GP*CP*AP*GP*TP*TP*CP*GP*GP*AP*C)-3' | dna | 14 | — | — |
| B | 5'-D(*GP*TP*CP*CP*GP*AP*TP*GP*CP*GP*TP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- DDI · Spiro[naphthalene-2(3H),3'(10'H)-pentaleno[1,2-b]naphthalene]-3,10'-dione, 2'-[(2-amino-2-deoxy-B-D-gulopyranosyl)oxy]-1,1',2',3'A,4,10'A-hexahydro-,(2'r,3'as,10'ar)-(9CI) · 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 · 637 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 1R4E · Solution structure of the Complex Formed between a Left-Handed Wedge-Shaped Spirocyclic… · 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 1R4E · PDBe 1R4E
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