Research workbench
Core of the alu domain of the mammalian srp
Analyse Core of the alu domain of the mammalian srp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1E8O
- Type
- protein + RNA
- Length
- 346 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Signal recognition particle 9 kda protein; Signal recognition particle 14 kda protein…
- UniProt
- P49458, P37108
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 9 kda protein | protein | 74 | 43% helix, 30% strand | P49458 |
| B | Signal recognition particle 14 kda protein | protein | 75 | 40% helix, 29% strand | P37108 |
| C | Signal recognition particle 9 kda protein | protein | 71 | 48% helix, 25% strand | P49458 |
| D | Signal recognition particle 14 kda protein | protein | 76 | 37% helix, 30% strand | P37108 |
| E | 7SL RNA | rna | 50 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 752 | 0.70 | 0.77 | 57 | empty |
| 2 | 64 | 0.27 | 0.73 | 10 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1583 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1495 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 591 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–E · 355 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–E · 273 Ų buried · 5 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1E8O · Core of the Alu domain of the mammalian SRP · the same entry in another collection · chain E against E, TM-score 1.00
- P37108 · AlphaFold monomer V2.0 prediction for signal recognition particle 14 kda protein (P37108) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P49458 · AlphaFold monomer V2.0 prediction for signal recognition particle 9 kda protein (P49458) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P49458
- Every structure of UniProt P37108
- Elsewhere: RCSB PDB 1E8O · PDBe 1E8O · UniProt P49458 · UniProt P37108
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