MolNFT v1 · #124989 · RNA
Crystal structure of the 16-mer doublestranded RNA. northeast structural genomics consortium (nesg) target RNA1
5KVJ · RNA (5'- R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)…: “Crystal structure of the 16-mer doublestranded RNA. northeast structural genomics consortium (nesg) target…”. X-ray diffraction, 1 ligand (ARG), 1 pocket (best…
- PDB
- 5KVJ
- Type
- RNA
- Length
- 32 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)-3'); RNA (5'…
- Ligands
- ARG
- Pockets
- 1 · best druggability 0.48
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RNA (5'- R(P*CP*CP*AP*UP*CP*CP*UP*CP*UP*AP*CP*AP*GP*GP*CP*G)-3') | rna | 16 | — | — |
| B | RNA (5'- R(P*CP*GP*CP*CP*UP*GP*UP*AP*GP*AP*GP*GP*AP*UP*GP*G)-3') | rna | 16 | — | — |
Ligands and binding sites
- ARG · Arginine · ligand · 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 | 351 | 0.48 | 0.72 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 102 hydrogen bonds · nucleic-nucleic
Compared structures
- 5KVJ · Crystal structure of the 16-mer doublestranded RNA. Northeast Structural Genomics… · 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 5KVJ · PDBe 5KVJ
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