Research workbench
Crystal structure of double-stranded RNA with four terminal gu wobble base pairs
Analyse Crystal structure of double-stranded RNA with four terminal gu wobble base pairs in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PCO
- Type
- RNA
- Length
- 50 nucleotides
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3')
- Ligands
- NCO, CL
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | RNA (5'-D(*GP*GP*UP*GP*GP*CP*UP*GP*UP*U)-3') | rna | 10 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 12 copies · chains A, B, C, D, E
- CL · Chloride ion · ion · 3 copies · chains A, B
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 | 127 | 0.34 | 0.72 | 12 | NCO |
| 2 | 120 | 0.32 | 0.72 | 21 | CL, NCO |
Interfaces
6 interfaces between chains.
- C–D · 499 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–B · 490 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- B–C · 89 Ų buried · 5 hydrogen bonds · nucleic-nucleic
- A–C · 80 Ų buried · 3 hydrogen bonds · nucleic-nucleic
- A–E · 77 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 4PCO · Crystal structure of double-stranded RNA with four terminal GU wobble base pairs · 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 4PCO · PDBe 4PCO
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