Research workbench
Crystal structure of the B-DNA hexamer ggcgcc with spermine
Analyse Crystal structure of the B-DNA hexamer ggcgcc with spermine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1F6C
- Type
- DNA
- Length
- 30 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*GP*CP*GP*CP*C)-3')
- Ligands
- SPM
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | DNA (5'-D(*GP*GP*CP*GP*CP*C)-3') | dna | 6 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · 2 copies · chains B, C, A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
7 interfaces between chains.
- B–C · 288 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- D–E · 281 Ų buried · 32 hydrogen bonds · nucleic-nucleic
- A–D · 132 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- C–D · 131 Ų buried · 0 hydrogen bonds · nucleic-nucleic
- B–E · 126 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 1F6C · Crystal structure of the B-DNA hexamer ggcgcc with spermine · 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 1F6C · PDBe 1F6C
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