MolNFT v1 · #124930 · DNA
Mis-pairing of unnatural base Z-G DNA duplex at pH 8.5
5KTV · DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*(1W5)P*GP*CP*G)-3'): “Mis-pairing of unnatural base Z-G DNA duplex at pH 8.5”. X-ray diffraction, 1 ligand (CA). MolNFT v1 #124930 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5KTV
- Type
- DNA
- Length
- 22 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*(1W5)P*GP*CP*G)-3')
- Ligands
- CA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(P*GP*CP*GP*AP*AP*TP*TP*(1W5)P*GP*CP*G)-3') | dna | 11 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 9 copies · 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 · 465 Ų buried · 38 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5KTV · Mis-pairing of unnatural base Z-G DNA duplex at pH 8.5 · 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 5KTV · PDBe 5KTV
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