Research workbench
Crystal structure of the cena-RNA hybrid octamer CE(GCGTAGCG) :R(CGCUACGC)
Analyse Crystal structure of the cena-RNA hybrid octamer CE(GCGTAGCG) :R(CGCUACGC) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KNC
- Type
- DNA + RNA
- Length
- 16 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR) P*(XGR)P*(XGR))-3'…
- Ligands
- XGR, MG
- Pockets
- 1 · best druggability 0.23
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-D(*(XGR)P*(XCR)P*(XGR)P*(XTR)P*(XAR)P*(XGR)P*(XCR) P*(XGR)P*(XGR))-3' | dna | 8 | — | — |
| B | 5'-R(*CP*GP*CP*UP*AP*CP*GP*C)-3' | rna | 8 | — | — |
Ligands and binding sites
- XGR · [(1R,4S,6S)-4-(2-amino-6-oxo-1,6-dihydro-9H-purin-9-yl)-6-hydroxycyclohex-2-en-1-yl]methyl dihydrogen phosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains 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 | 51 | 0.23 | 0.72 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 405 Ų buried · 36 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 3KNC · Crystal structure of the CeNA-RNA hybrid octamer ce(GCGTAGCG):r(CGCUACGC) · 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 3KNC · PDBe 3KNC
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