Research workbench
The C92U mutant c-di-GMP-I riboswitch bound to pGpA
Analyse The C92U mutant c-di-GMP-I riboswitch bound to pGpA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UD3
- Type
- protein + RNA
- Length
- 181 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.1
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- U1 small nuclear ribonucleoprotein A; RNA (92-mer); RNA (5'-R(P*GP*A)-3')
- UniProt
- P09012
- Ligands
- MG
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · resolution 3.1 · 3 distinct chains · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | U1 small nuclear ribonucleoprotein A | protein | 87 | 25% helix, 21% strand | P09012 |
| R | RNA (92-mer) | rna | 92 | — | — |
| A | RNA (5'-R(P*GP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 715 | 0.70 | 0.78 | 48 | empty |
| 2 | 541 | 0.66 | 0.78 | 32 | empty |
| 3 | 415 | 0.58 | 0.76 | 28 | MG |
Interfaces
2 interfaces between chains.
- P–R · 989 Ų buried · 23 hydrogen bonds · protein-nucleic
- R–A · 485 Ų buried · 23 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P09012
- Elsewhere: RCSB PDB 3UD3 · PDBe 3UD3 · UniProt P09012
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