Research workbench
Factors affecting sequence selectivity on nogalamycin intercalation: the crystal structure of D(TGTACA)- nogalamycin
Analyse Factors affecting sequence selectivity on nogalamycin intercalation: the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 258D
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*TP*AP*CP*A)-3')
- Ligands
- NGM, SPM, NA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(*TP*GP*TP*AP*CP*A)-3') | dna | 6 | — | — |
Ligands and binding sites
- NGM · Nogalamycin · ligand · 4 copies · chains A, B, C, D
- SPM · Spermine · ligand · chains A
- NA · Sodium ion · metal · chains B
- ACT · Acetate ion · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
2 interfaces between chains.
- A–B · 279 Ų buried · 18 hydrogen bonds · nucleic-nucleic
- C–D · 279 Ų buried · 18 hydrogen bonds · nucleic-nucleic
Compared structures
- 258D · Factors affecting sequence selectivity on nogalamycin intercalation: the crystal… · the same entry in another collection · chain B against B, 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 258D · PDBe 258D
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