Research workbench
Crystal structure of a glycine riboswitch from fusobacterium nucleatum
Analyse Crystal structure of a glycine riboswitch from fusobacterium nucleatum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P49
- Type
- protein + RNA
- Length
- 261 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycine riboswitch; U1 small nuclear ribonucleoprotein a
- UniProt
- P09012
- Ligands
- GLY, MG
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycine riboswitch | rna | 169 | — | — |
| B | U1 small nuclear ribonucleoprotein a | protein | 92 | 27% helix, 24% strand | P09012 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 921 | 0.71 | 0.77 | 38 | empty |
| 2 | 568 | 0.71 | 0.80 | 28 | empty |
| 3 | 892 | 0.67 | 0.75 | 49 | MG |
| 4 | 303 | 0.62 | 0.81 | 28 | empty |
| 5 | 57 | 0.55 | 0.90 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 948 Ų buried · 18 hydrogen bonds · protein-nucleic
Compared structures
- 3P49 · Crystal Structure of a Glycine Riboswitch from Fusobacterium nucleatum · 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
- Every structure of UniProt P09012
- Elsewhere: RCSB PDB 3P49 · PDBe 3P49 · UniProt P09012
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