MolNFT v1 · #88790 · protein + RNA
Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus ires reveal the ires in the translocated state
4D5N · Eukaryotic peptide chain release factor subunit 1: “Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket paralysis virus ires…”. Electron microscopy, 15 pockets (best druggability 0.66). MolNFT v1…
- PDB
- 4D5N
- Type
- protein + RNA
- Length
- 637 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic peptide chain release factor subunit 1; Cricket paralysis virus ires RNA
- UniProt
- P62495
- Pockets
- 15 · best druggability 0.66
Structure
electron microscopy · 2 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic peptide chain release factor subunit 1 | protein | 436 | 39% helix, 22% strand | P62495 |
| X | Cricket paralysis virus ires RNA | rna | 201 | — | — |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 407 | 0.66 | 0.80 | 23 | empty |
| 2 | 344 | 0.64 | 0.79 | 41 | empty |
| 3 | 107 | 0.60 | 0.86 | 18 | empty |
| 4 | 102 | 0.60 | 0.86 | 19 | empty |
| 5 | 521 | 0.59 | 0.74 | 47 | empty |
Interfaces
1 interface between chains.
- A–X · 195 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4D5N · Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket… · the same entry in another collection · chain X against X, TM-score 1.00
- P62495 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor subunit 1… · a predicted model of the same protein · chain A against A, TM-score 0.66
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 P62495
- Elsewhere: RCSB PDB 4D5N · PDBe 4D5N · UniProt P62495
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