Research workbench
Crystal structure of SRP19 in complex with the S domain of signal recognition particle RNA
Analyse Crystal structure of SRP19 in complex with the S domain of signal recognition… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L9A
- Type
- protein + RNA
- Length
- 213 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle RNA S domain; Signal recognition particle 19 kda protein
- UniProt
- Q58440
- Ligands
- MMC, MG
- Pockets
- 8 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Signal recognition particle RNA S domain | rna | 126 | — | — |
| A | Signal recognition particle 19 kda protein | protein | 87 | 33% helix, 7% strand | Q58440 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 758 | 0.71 | 0.78 | 51 | MG |
| 2 | 741 | 0.64 | 0.75 | 35 | MG |
| 3 | 208 | 0.50 | 0.77 | 16 | empty |
| 4 | 152 | 0.37 | 0.72 | 11 | empty |
| 5 | 163 | 0.37 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 1132 Ų buried · 36 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1L9A · Crystal structure of SRP19 in complex with the S domain of signal recognition particle RNA · the same entry in another collection · chain B against B, TM-score 1.00
- Q58440 · AlphaFold monomer V2.0 prediction for signal recognition particle 19 kda protein (Q58440) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q58440
- Elsewhere: RCSB PDB 1L9A · PDBe 1L9A · UniProt Q58440
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