Research workbench
2'-seme-a modified DNA decamer
Analyse 2'-seme-a modified DNA decamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3IFF
- Type
- DNA
- Length
- 20 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*TP*AP*CP*GP*CP*GP*TP*(XUA)P*C)-3')
- Ligands
- MG
- Pockets
- 1 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*GP*TP*AP*CP*GP*CP*GP*TP*(XUA)P*C)-3') | dna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, A
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 | 124 | 0.34 | 0.73 | 12 | MG |
Interfaces
1 interface between chains.
- A–B · 478 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3IFF · 2'-SeMe-A modified DNA decamer · 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 3IFF · PDBe 3IFF
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