Research workbench
Structure of R-gna dodecamer
Analyse Structure of R-gna dodecamer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V1K
- Type
- RNA
- Length
- 22 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3')
- Ligands
- 8RJ
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | RNA (5'-R(*CP*GP*CP*GP*AP*AP*(5BU)P*(8RJ)P*AP*GP*CP*G)-3') | rna | 11 | — | — |
Ligands and binding sites
- 8RJ · (R)-1'-(2',3'-dihydroxypropyl)-thymine · ligand · 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 | 50 | 0.27 | 0.75 | 9 | empty |
Interfaces
1 interface between chains.
- A–B · 681 Ų buried · 54 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nucleotide modification).
Compared structures
- 5V1K · Structure of R-GNA dodecamer · 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 5V1K · PDBe 5V1K
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