MolNFT v1 · #21043 · protein + RNA
Structure of the signal recognition particle interacting with the elongation-arrested ribosome
1RY1 · Srp alu domain: “Structure of the signal recognition particle interacting with the elongation-arrested ribosome”. Electron microscopy, 18 pockets (best druggability 0.77). MolNFT v1 #21043 on GenesisL1: 3D structure, binding sites…
- PDB
- 1RY1
- Type
- protein + RNA
- Length
- 977 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Srp alu domain; Srp S domain; Srp RNA; SRP9; SRP14; SRP19; SRP54NG; SRP54M; Signal…
- UniProt
- P37108
- Pockets
- 18 · best druggability 0.77
Structure
electron microscopy · 14 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Srp alu domain | rna | 49 | — | — |
| A | Srp S domain | rna | 128 | — | — |
| M | Srp RNA | rna | 27 | — | — |
| N | Srp RNA | rna | 31 | — | — |
| O | Srp RNA | rna | 24 | — | — |
| P | Srp RNA | rna | 19 | — | — |
| Q | Srp RNA | rna | 12 | — | — |
| R | Srp RNA | rna | 12 | — | — |
| C | SRP9 | protein | 71 | 48% helix, 25% strand | — |
| D | SRP14 | protein | 76 | 37% helix, 30% strand | P37108 |
| B | SRP19 | protein | 107 | 30% helix, 16% strand | — |
| U | SRP54NG | protein | 294 | 54% helix, 14% strand | — |
| W | SRP54M | protein | 109 | 65% helix, 1% strand | — |
| S | Signal sequence peptide | protein | 18 | 78% helix, 0% strand | — |
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 883 | 0.77 | 0.81 | 43 | empty |
| 2 | 1123 | 0.75 | 0.78 | 77 | empty |
| 3 | 732 | 0.70 | 0.78 | 31 | empty |
| 4 | 717 | 0.70 | 0.78 | 51 | empty |
| 5 | 1019 | 0.68 | 0.74 | 51 | empty |
Interfaces
25 interfaces between chains.
- C–D · 1497 Ų buried · 18 hydrogen bonds · protein-protein
- M–N · 1179 Ų buried · 66 hydrogen bonds · nucleic-nucleic
- A–B · 975 Ų buried · 43 hydrogen bonds · protein-nucleic
- O–P · 945 Ų buried · 55 hydrogen bonds · nucleic-nucleic
- U–W · 816 Ų buried · 44 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 isopeptide, 1 modified (isopeptide, nucleotide modification).
Compared structures
- 1RY1 · Structure of the signal recognition particle interacting with the elongation-arrested… · the same entry in another collection · chain S against S, 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 P37108
- Elsewhere: RCSB PDB 1RY1 · PDBe 1RY1 · UniProt P37108
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