Research workbench
DNA helical wire containing HG(II)
Analyse DNA helical wire containing HG(II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IUE
- Type
- DNA
- Length
- 118 nucleotides
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*TP*TP*GP*C)-3')
- Ligands
- HG
- Pockets
- 3 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, M, B, N, C, O, D, P, E, Q, R, G, T, H, U, I, V, J, W, K, X, Y | DNA (5'-D(*TP*TP*TP*GP*C)-3') | dna | 5 | — | — |
| F, L | DNA (5'-D(*TP*TP*TP*GP*C)-3') | dna | 4 | — | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 48 copies · chains A, M, C, B, N, R, O, D, P, F, W, E, Q, J, V, G, T, Y, H, U, I, K, X, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.34 | 0.76 | 13 | empty |
| 2 | 64 | 0.29 | 0.74 | 13 | empty |
| 3 | 52 | 0.27 | 0.75 | 10 | empty |
Interfaces
46 interfaces between chains.
- G–T · 199 Ų buried · 7 hydrogen bonds · nucleic-nucleic
- E–Q · 196 Ų buried · 9 hydrogen bonds · nucleic-nucleic
- B–N · 196 Ų buried · 10 hydrogen bonds · nucleic-nucleic
- J–W · 193 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- A–M · 193 Ų buried · 11 hydrogen bonds · nucleic-nucleic
Compared structures
- 6IUE · DNA helical wire containing Hg(II) · 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 6IUE · PDBe 6IUE
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.