Research workbench
Crystal structure of a 19 base pair copy control related RNA duplex
Analyse Crystal structure of a 19 base pair copy control related RNA duplex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1QC0
- Type
- RNA
- Length
- 57 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3'; 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3'…
- Ligands
- NH4
- Pockets
- 1 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*AP*GP*CP*GP*GP*UP*GP*C)-3' | rna | 9 | — | — |
| B | 5'-R(GP*CP*AP*CP*CP*GP*CP*UP*AP*C)-3' | rna | 10 | — | — |
| C | 5'-R(*GP*CP*AP*CP*CP*GP*UP*UP*GP*GP*UP*AP*GP*CP*GP*GP*UP*GP *C)-3' | rna | 19 | — | — |
| D | 5'-R(*GP*CP*AP*CP*CP*GP*CP*UP*AP*CP*CP*AP*AP*CP*GP*GP*UP*GP *C)-3' | rna | 19 | — | — |
Ligands and binding sites
- NH4 · Ammonium ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.52 | 0.72 | 30 | empty |
Interfaces
5 interfaces between chains.
- C–D · 921 Ų buried · 115 hydrogen bonds · nucleic-nucleic
- A–B · 455 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- B–D · 89 Ų buried · 2 hydrogen bonds · nucleic-nucleic
- A–C · 85 Ų buried · 1 hydrogen bond · nucleic-nucleic
- B–C · 83 Ų buried · 2 hydrogen bonds · nucleic-nucleic
Compared structures
- 1QC0 · Crystal structure of a 19 base pair copy control related RNA duplex · 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 1QC0 · PDBe 1QC0
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