Research workbench
Cryo-EM of a pretermination complex with ERF1 and ERF3
Analyse Cryo-EM of a pretermination complex with ERF1 and ERF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CRN
- Type
- protein
- Length
- 851 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ERF3 in ribosome bound ERF1-ERF3-gdpnp complex; ERF1 in ribosome-bound ERF1-ERF3-gdpnp…
- UniProt
- P05453, P12385
- Ligands
- GNP
- Pockets
- 11 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 21% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | ERF3 in ribosome bound ERF1-ERF3-gdpnp complex | protein | 430 | 12% helix, 23% strand | P05453 |
| X | ERF1 in ribosome-bound ERF1-ERF3-gdpnp complex | protein | 421 | 29% helix, 16% strand | P12385 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1076 | 0.83 | 0.84 | 124 | empty |
| 2 | 826 | 0.80 | 0.83 | 89 | empty |
| 3 | 208 | 0.65 | 0.83 | 24 | empty |
| 4 | 320 | 0.64 | 0.80 | 38 | empty |
| 5 | 124 | 0.63 | 0.87 | 25 | empty |
Interfaces
1 interface between chains.
- P–X · 1405 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 covalent (covalent ligand).
Compared structures
- 4CRN · Cryo-EM of a pretermination complex with eRF1 and eRF3 · the same entry in another collection · chain P against P, TM-score 1.00
- P12385 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor subunit 1… · a predicted model of the same protein · chain X against A, TM-score 0.83
- P05453 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor GTP-binding… · a predicted model of the same protein · chain P against A, TM-score 0.81
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 P05453
- Every structure of UniProt P12385
- Elsewhere: RCSB PDB 4CRN · PDBe 4CRN · UniProt P05453 · UniProt P12385
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