Research workbench
Methylation of cytosine at C5 in a cpg sequence context causes a conformational switch of a BENZO[A]PYRENE diol epoxide-N2-guanine adduct in DNA from a minor groove alignment to intercalation with base displacement
Analyse Methylation of cytosine at C5 in a cpg sequence context causes a conformational… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Y9H
- Type
- DNA
- Length
- 22 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3'…
- Ligands
- BAP
- Pockets
- 1 · best druggability 0.33
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*CP*AP*TP*(5CM)P*(BPG)P*CP*TP*AP*CP*C)-3' | dna | 11 | — | — |
| B | 5'-D(*GP*GP*TP*AP*GP*CP*GP*AP*TP*GP*G)-3' | dna | 11 | — | — |
Ligands and binding sites
- BAP · 1,2,3-trihydroxy-1,2,3,4-tetrahydrobenzo[a]pyrene · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.33 | 0.75 | 9 | BAP |
Interfaces
1 interface between chains.
- A–B · 575 Ų buried · 59 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 1Y9H · Methylation of cytosine at C5 in a CpG sequence context causes a conformational switch of… · 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 1Y9H · PDBe 1Y9H
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.