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Crystal structure of DNA duplex containing two consecutive mercury- mediated base pairs
Analyse Crystal structure of DNA duplex containing two consecutive mercury- mediated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R6M
- Type
- DNA
- Length
- 60 nucleotides
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3'); DNA…
- Ligands
- HG
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | DNA (5'-D(P*GP*GP*AP*CP*TP*TP*CP*GP*CP*G)-3') | dna | 10 | — | — |
| B, D, F | DNA (5'-D(P*CP*GP*CP*GP*TP*TP*GP*TP*CP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- HG · Mercury (II) ion · metal · 6 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 309 | 0.52 | 0.74 | 24 | empty |
| 2 | 66 | 0.25 | 0.72 | 8 | empty |
Interfaces
8 interfaces between chains.
- C–D · 452 Ų buried · 37 hydrogen bonds · nucleic-nucleic
- A–B · 396 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- E–F · 391 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- B–F · 164 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–F · 154 Ų buried · 6 hydrogen bonds · nucleic-nucleic
Compared structures
- 4R6M · Crystal Structure of DNA Duplex Containing Two Consecutive Mercury-mediated Base Pairs · 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 4R6M · PDBe 4R6M
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