Research workbench
Human alu RNA retrotransposition complex in the ribosome-stalling conformation
Analyse Human alu RNA retrotransposition complex in the ribosome-stalling conformation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AOX
- Type
- protein + RNA
- Length
- 489 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
- Ligands
- MG, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Signal recognition particle 9 kda protein | protein | 76 | 41% helix, 29% strand | P49458 |
| B | Signal recognition particle 14 kda protein | protein | 86 | 34% helix, 26% strand | P37108 |
| C | Alu jo consensus RNA | rna | 85 | — | — |
| D | Signal recognition particle 9 kda protein | protein | 73 | 47% helix, 29% strand | P49458 |
| E | Signal recognition particle 14 kda protein | protein | 84 | 38% helix, 27% strand | P37108 |
| F | Alu jo consensus RNA | rna | 85 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains C, F
- SO4 · Sulfate ion · ion · 2 copies · chains C, F
- ACT · Acetate ion · additive · 2 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.78 | 0.81 | 80 | SO4, MG |
| 2 | 1069 | 0.77 | 0.80 | 71 | SO4, MG |
| 3 | 60 | 0.67 | 0.96 | 17 | ACT |
| 4 | 193 | 0.51 | 0.77 | 28 | empty |
| 5 | 57 | 0.48 | 0.86 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1590 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1550 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 872 Ų buried · 20 hydrogen bonds · protein-nucleic
- E–F · 872 Ų buried · 24 hydrogen bonds · protein-nucleic
- A–C · 594 Ų buried · 16 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5AOX · Human Alu RNA retrotransposition complex in the ribosome-stalling conformation · the same entry in another collection · chain F against F, TM-score 1.00
- P49458 · AlphaFold monomer V2.0 prediction for signal recognition particle 9 kda protein (P49458) · a predicted model of the same protein · chain D against A, TM-score 0.99
- P37108 · AlphaFold monomer V2.0 prediction for signal recognition particle 14 kda protein (P37108) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 5AOX · PDBe 5AOX · UniProt P49458 · UniProt P37108
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