MolNFT v1 · #153831 · DNA
Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster
6JR4 · DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3'): “Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster”. X-ray diffraction, 2 ligands (AG, CA). MolNFT v1 #153831 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 6JR4
- Type
- DNA
- Length
- 40 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3')
- Ligands
- AG, CA
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | DNA (5'-D(*CP*AP*CP*CP*TP*AP*GP*CP*GP*A)-3') | dna | 10 | — | — |
Ligands and binding sites
- AG · Silver ion · metal · 38 copies · chains A, B, D, C
- CA · Calcium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
6 interfaces between chains.
- C–D · 427 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- A–B · 426 Ų buried · 24 hydrogen bonds · nucleic-nucleic
- A–C · 122 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–D · 60 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 56 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 6JR4 · Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster · 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 6JR4 · PDBe 6JR4
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