MolNFT v1 · #80549 · DNA
Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 a resolution
3U08 · 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3': “Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 a resolution”. X-ray diffraction, 2 ligands (D63, MG), 1 pocket (best druggability 0.24). MolNFT v1 #80549 on GenesisL1: 3D…
- PDB
- 3U08
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'
- Ligands
- D63, MG
- Pockets
- 1 · best druggability 0.24
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3' | dna | 12 | — | — |
Ligands and binding sites
- D63 · 4'-(5-carbamimidoyl-1H-benzimidazol-2-yl)biphenyl-4-carboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · 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 | 52 | 0.24 | 0.72 | 12 | D63 |
Interfaces
1 interface between chains.
- A–B · 567 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Compared structures
- 3U08 · Crystal structure of DB1963-D(CGCGAATTCGCG)2 complex at 1.25 A resolution · 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 3U08 · PDBe 3U08
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