Research workbench
Crystal structure of a minimal, native (U39) all-RNA hairpin ribozyme
Analyse Crystal structure of a minimal, native (U39) all-RNA hairpin ribozyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D2K
- Type
- RNA
- Length
- 61 nucleotides
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3'…
- Ligands
- NCO, SO4
- Pockets
- 3 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*G)-3' | rna | 13 | — | — |
| B | 5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3' | rna | 12 | — | — |
| C | 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)- 3' | rna | 17 | — | — |
| D | 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*UP*AP*UP*UP*AP*CP*CP*UP*GP*CP *C)-3' | rna | 19 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 2 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 202 | 0.42 | 0.74 | 18 | NCO |
| 2 | 159 | 0.40 | 0.74 | 20 | empty |
| 3 | 121 | 0.34 | 0.73 | 16 | empty |
Interfaces
6 interfaces between chains.
- C–D · 882 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- A–B · 651 Ų buried · 53 hydrogen bonds · nucleic-nucleic
- A–D · 352 Ų buried · 11 hydrogen bonds · nucleic-nucleic
- B–C · 199 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- A–C · 183 Ų buried · 8 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 2D2K · Crystal Structure of a minimal, native (U39) all-RNA hairpin ribozyme · 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 2D2K · PDBe 2D2K
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