MolNFT v1 · #43392 · DNA
N2-DG:N2-dg interstrand cross-link induced by trans-4-hydroxynonenal
2LBI · DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'): “N2-DG:N2-dg interstrand cross-link induced by trans-4-hydroxynonenal”. Solution nmr, 1 ligand (HND), 1 pocket (best druggability 0.29). MolNFT v1 #43392 on GenesisL1: 3D…
- PDB
- 2LBI
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3'); DNA…
- Ligands
- HND
- Pockets
- 1 · best druggability 0.29
Structure
solution nmr · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*GP*CP*TP*AP*GP*CP*GP*AP*GP*TP*CP*C)-3') | dna | 12 | — | — |
| B | DNA (5'-D(*GP*GP*AP*CP*TP*CP*GP*CP*TP*AP*GP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- HND · (4S)-nonane-1,4-diol · 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 | 72 | 0.29 | 0.74 | 11 | HND |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 46 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2LBI · N2-dG:N2-dG interstrand cross-link induced by trans-4-hydroxy nal · 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 2LBI · PDBe 2LBI
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