Research workbench
First crystal structure of a RNA nanosquare
Analyse First crystal structure of a RNA nanosquare in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P59
- Type
- RNA
- Length
- 98 nucleotides
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU) P*G)-3'); RNA…
- Ligands
- NCO, MG
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU) P*G)-3') | rna | 15 | — | — |
| B, D, F, H | RNA (5'-R(*CP*CP*GP*GP*CP*AP*GP*CP*CP*U)-3') | rna | 10 | — | — |
| G | RNA (5'-R(*CP*CP*GP*GP*AP*GP*GP*AP*AP*CP*UP*AP*CP*(5BU) P*G)-3') | rna | 13 | — | — |
Ligands and binding sites
- NCO · Cobalt hexammine(iii) · ligand · 10 copies · chains A, D, B, G, C, E, F, H
- MG · Magnesium ion · metal · 2 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.58 | 0.74 | 26 | MG, NCO |
| 2 | 455 | 0.54 | 0.73 | 26 | NCO |
| 3 | 353 | 0.52 | 0.74 | 31 | NCO |
| 4 | 53 | 0.24 | 0.73 | 8 | NCO |
Interfaces
16 interfaces between chains.
- E–F · 405 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- A–B · 401 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- C–D · 375 Ų buried · 33 hydrogen bonds · nucleic-nucleic
- G–H · 374 Ų buried · 34 hydrogen bonds · nucleic-nucleic
- A–D · 258 Ų buried · 24 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3P59 · First Crystal Structure of a RNA Nanosquare · 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 3P59 · PDBe 3P59
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