Research workbench
Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster (G7I/G9I mutant)
Analyse Crystal structure of a nir-emitting DNA-stabilized AG16 nanocluster (G7I/G9I… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XLW
- Type
- DNA
- Length
- 119 nucleotides
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3')
- Ligands
- AG
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, G, H, I, J, K, L | DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3') | dna | 10 | — | — |
| F | DNA (5'-D(*CP*AP*CP*CP*TP*AP*IP*CP*IP*A)-3') | dna | 9 | — | — |
Ligands and binding sites
- AG · Silver ion · metal · 108 copies · chains A, B, I, C, D, E, F, G, H, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.51 | 0.83 | 24 | AG |
| 2 | 107 | 0.45 | 0.80 | 23 | AG |
| 3 | 111 | 0.36 | 0.74 | 15 | empty |
| 4 | 67 | 0.27 | 0.73 | 11 | empty |
Interfaces
22 interfaces between chains.
- A–B · 477 Ų buried · 20 hydrogen bonds · nucleic-nucleic
- G–H · 469 Ų buried · 23 hydrogen bonds · nucleic-nucleic
- C–D · 442 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- E–F · 409 Ų buried · 19 hydrogen bonds · nucleic-nucleic
- I–J · 398 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Compared structures
- 7XLW · Crystal structure of a NIR-emitting DNA-stabilized Ag16 nanocluster (G7I/G9I mutant) · 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 7XLW · PDBe 7XLW
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