Research workbench
Structure of the oligonucleotide D(CGTATATACG) as a site specific complex with nickel ions
Analyse Structure of the oligonucleotide D(CGTATATACG) as a site specific complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 446D
- Type
- DNA
- Length
- 37 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3')
- Ligands
- NI
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3') | dna | 9 | — | — |
| D | DNA (5'-D(*CP*GP*TP*AP*TP*AP*TP*AP*CP*G)-3') | dna | 10 | — | — |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 9 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- C–D · 358 Ų buried · 26 hydrogen bonds · nucleic-nucleic
- A–B · 356 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- A–C · 180 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- B–D · 178 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- B–C · 174 Ų buried · 3 hydrogen bonds · nucleic-nucleic
Compared structures
- 446D · Structure of the oligonucleotide D(CGTATATACG) as a site specific complex with nickel ions · the same entry in another collection · chain D against D, 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 446D · PDBe 446D
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