Research workbench
Solution structure of the yeast translation initiation factor EIF4E in complex with M7GDP and EIF4GI residues 393 to 490
Analyse Solution structure of the yeast translation initiation factor EIF4E in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RF8
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E; Eukaryotic initiation factor 4F subunit P150
- UniProt
- P07260, P39935
- Ligands
- MTN, M7G
- Pockets
- 3 · best druggability 0.55
Structure
solution nmr · 2 distinct chains · 28% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 213 | 26% helix, 19% strand | P07260 |
| B | Eukaryotic initiation factor 4F subunit P150 | protein | 100 | 32% helix, 1% strand | P39935 |
Ligands and binding sites
- MTN · S-[(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl] methanesulfonothioate · ligand · 4 copies · chains A, B
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.55 | 0.81 | 24 | empty |
| 2 | 119 | 0.43 | 0.77 | 23 | M7G |
| 3 | 90 | 0.39 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2126 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 1RF8 · Solution structure of the yeast translation initiation factor eIF4E in complex with m7GDP… · the same entry in another collection · chain A against A, TM-score 1.00
- P07260 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P07260) · a predicted model of the same protein · chain A against A, TM-score 0.76
- P39935 · AlphaFold monomer V2.0 prediction for eukaryotic initiation factor 4F subunit P150… · a predicted model of the same protein · chain B against A, TM-score 0.49
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 P07260
- Every structure of UniProt P39935
- Elsewhere: RCSB PDB 1RF8 · PDBe 1RF8 · UniProt P07260 · UniProt P39935
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.