MolNFT v1 · #88336 · protein
Cryo-EM of a pre-recycling complex with ERF1 and ABCE1
4CRM · Translation initiation factor RLI1: “Cryo-EM of a pre-recycling complex with ERF1 and ABCE1”. Electron microscopy, 4 ligands (SF4, ATP, ADP), 14 pockets (best druggability 0.79). MolNFT v1 #88336 on GenesisL1: 3D structure, binding…
- PDB
- 4CRM
- Type
- protein
- Length
- 890 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Translation initiation factor RLI1; Eukaryotic peptide chain release factor subunit 1
- UniProt
- Q03195, P12385
- Ligands
- SF4, ATP, ADP, MG
- Pockets
- 14 · best druggability 0.79
Structure
electron microscopy · 2 distinct chains · 33% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Translation initiation factor RLI1 | protein | 608 | 33% helix, 18% strand | Q03195 |
| X | Eukaryotic peptide chain release factor subunit 1 | protein | 282 | 34% helix, 21% strand | P12385 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains P
- ATP · Adenosine-5'-triphosphate · ligand · chains P
- ADP · Adenosine-5'-diphosphate · ligand · chains P
- MG · Magnesium ion · metal · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 323 | 0.79 | 0.89 | 53 | empty |
| 2 | 1197 | 0.75 | 0.78 | 118 | ATP, ADP |
| 3 | 77 | 0.66 | 0.92 | 25 | empty |
| 4 | 78 | 0.60 | 0.89 | 26 | SF4 |
| 5 | 360 | 0.55 | 0.74 | 40 | empty |
Interfaces
1 interface between chains.
- P–X · 282 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 1 isopeptide (covalent ligand, isopeptide).
Compared structures
- 4CRM · Cryo-EM of a pre-recycling complex with eRF1 and ABCE1 · the same entry in another collection · chain P against P, TM-score 1.00
- Q03195 · AlphaFold monomer V2.0 prediction for translation initiation factor RLI1 (Q03195) · a predicted model of the same protein · chain P against A, TM-score 0.91
- 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 0.52
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 Q03195
- Every structure of UniProt P12385
- Elsewhere: RCSB PDB 4CRM · PDBe 4CRM · UniProt Q03195 · UniProt P12385
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