MolNFT v1 · #28338 · DNA
Crystal structure of the a-DNA GCGTAT*CGC with a 2'-O-[2-(N, N-DIMETHYLAMINOOXY)ETHYL] thymidine (T*)
1YB9 · 5'-D(*GP*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3'): “Crystal structure of the a-DNA GCGTAT*CGC with a 2'-O-[2-(N, N-DIMETHYLAMINOOXY)ETHYL] thymidine (T*)”. X-ray diffraction, 1 ligand (SPM), 1 pocket (best druggability 0.26). MolNFT v1…
- PDB
- 1YB9
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3')
- Ligands
- SPM
- Pockets
- 1 · best druggability 0.26
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-D(*GP*CP*GP*TP*AP*(2OT)P*AP*CP*GP*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- SPM · Spermine · ligand · chains 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 | 75 | 0.26 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 523 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1YB9 · Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(N,N-dimethylaminooxy)ethyl]… · 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 1YB9 · PDBe 1YB9
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