Research workbench
Crystal structure of a signal recognition particle alu domain in the elongation arrest conformation
Analyse Crystal structure of a signal recognition particle alu domain in the elongation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UYJ
- Type
- protein + RNA
- Length
- 533 residues
- Chains
- 6
- 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
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Signal recognition particle 9 kda protein | protein | 74 | 42% helix, 26% strand | P49458 |
| B | Signal recognition particle 14 kda protein | protein | 82 | 39% helix, 29% strand | P37108 |
| D | Signal recognition particle 14 kda protein | protein | 83 | 36% helix, 30% strand | P37108 |
| R, S | Srp RNA | rna | 110 | — | — |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.79 | 0.82 | 73 | empty |
| 2 | 1050 | 0.75 | 0.78 | 54 | empty |
| 3 | 733 | 0.62 | 0.74 | 37 | empty |
| 4 | 656 | 0.62 | 0.74 | 46 | empty |
| 5 | 128 | 0.41 | 0.76 | 18 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1506 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1429 Ų buried · 16 hydrogen bonds · protein-protein
- B–R · 810 Ų buried · 17 hydrogen bonds · protein-nucleic
- D–S · 756 Ų buried · 17 hydrogen bonds · protein-nucleic
- C–S · 586 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 14 modified (engineered, nucleotide modification).
Compared structures
- 4UYJ · Crystal structure of a Signal Recognition Particle Alu domain in the elongation arrest… · the same entry in another collection · chain S against S, 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 0.97
- 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 0.96
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 P49458
- Every structure of UniProt P37108
- Elsewhere: RCSB PDB 4UYJ · PDBe 4UYJ · UniProt P49458 · UniProt P37108
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.