Research workbench
Crystal structure of an RNA duplex with uridine bulges
Analyse Crystal structure of an RNA duplex with uridine bulges in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1J9H
- Type
- RNA
- Length
- 36 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3'
- Ligands
- CA
- Pockets
- 2 · best druggability 0.39
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5'-R(*GP*UP*GP*UP*CP*GP*(CBR)P*AP*C)-3' | rna | 9 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.39 | 0.74 | 12 | empty |
| 2 | 131 | 0.36 | 0.73 | 10 | empty |
Interfaces
2 interfaces between chains.
- A–B · 460 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- C–D · 459 Ų buried · 34 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 1J9H · Crystal Structure of an RNA Duplex with Uridine Bulges · 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 1J9H · PDBe 1J9H
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