MolNFT v1 · #170879 · protein
Translation initiation factor 4E in complex with BN7GPPPG mRNA 5' cap analog
6YLR · Eukaryotic translation initiation factor 4E: “Translation initiation factor 4E in complex with BN7GPPPG mRNA 5' cap analog”. X-ray diffraction, 1 ligand (OYE), 7 pockets (best druggability 0.66). MolNFT v1 #170879 on GenesisL1: 3D…
- PDB
- 6YLR
- Type
- protein
- Length
- 354 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- OYE
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 184 | 32% helix, 29% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 170 | 31% helix, 29% strand | P63073 |
Ligands and binding sites
- OYE · bn7GpppG mRNA 5' cap analog · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.66 | 0.81 | 29 | empty |
| 2 | 154 | 0.54 | 0.80 | 32 | empty |
| 3 | 117 | 0.52 | 0.82 | 24 | empty |
| 4 | 129 | 0.50 | 0.79 | 19 | empty |
| 5 | 84 | 0.42 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1155 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6YLR · Translation initiation factor 4E in complex with bn7GpppG mRNA 5' cap analog · 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 6YLR · PDBe 6YLR · UniProt P63073
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