MolNFT v1 · #11129 · DNA
Solution structure of a trans-opened (10S)-da adduct of (+)-(7S,8R,9S, 10R)-7,8-dihydroxy-9,10-epoxy-7,8,9,10-TETRAHYDROBENZO[A]PYRENE in a fully complementary DNA duplex
1JDG · 5'-D(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3': “Solution structure of a trans-opened (10S)-da adduct of (+)-(7S,8R,9S…”. Solution nmr, 1 ligand (BPA). MolNFT v1 #11129 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JDG
- Type
- DNA
- Length
- 22 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3'; 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3'
- Ligands
- BPA
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*CP*GP*GP*TP*CP*(BPA)AP*CP*GP*AP*GP*G)-3' | dna | 11 | — | — |
| B | 5'-D(*CP*CP*TP*CP*GP*TP*GP*AP*CP*CP*G)-3' | dna | 11 | — | — |
Ligands and binding sites
- BPA · 7S,8R,9R-trihydroxy-7,8,9,10-tetrahydro benzo[a]pyrene · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 526 Ų buried · 71 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1JDG · Solution Structure of a Trans-Opened (10S)-dA Adduct 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 1JDG · PDBe 1JDG
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