Research workbench
Cocrystal structure of the messenger RNA 5' cap-binding protein (EIF4E) bound to 7-methylgpppg
Analyse Cocrystal structure of the messenger RNA 5' cap-binding protein (EIF4E) bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L8B
- Type
- protein
- Length
- 367 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- MGP
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 177 | 34% helix, 33% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 190 | 33% helix, 27% strand | P63073 |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.71 | 0.80 | 49 | empty |
| 2 | 54 | 0.69 | 0.96 | 15 | empty |
| 3 | 278 | 0.67 | 0.83 | 42 | empty |
| 4 | 152 | 0.51 | 0.79 | 30 | MGP |
| 5 | 136 | 0.48 | 0.78 | 21 | MGP |
Interfaces
1 interface between chains.
- A–B · 932 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 1L8B · Cocrystal Structure of the Messenger RNA 5' Cap-binding Protein (eIF4E) bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- P63073 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P63073) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P63073
- Elsewhere: RCSB PDB 1L8B · PDBe 1L8B · UniProt P63073
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