MolNFT v1 · #150130 · protein
Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (M7GPPPAPG)
6GKJ · Eukaryotic translation initiation factor 4E: “Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (M7GPPPAPG)”. X-ray diffraction, 1 ligand (MGP), 6 pockets (best druggability 0.51). MolNFT v1 #150130 on…
- PDB
- 6GKJ
- Type
- protein
- Length
- 721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- MGP
- Pockets
- 6 · best druggability 0.51
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 184 | 34% helix, 28% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 182 | 36% helix, 29% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 174 | 33% helix, 28% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 181 | 33% helix, 29% strand | P63073 |
Ligands and binding sites
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.51 | 0.80 | 34 | empty |
| 2 | 180 | 0.51 | 0.77 | 23 | empty |
| 3 | 162 | 0.51 | 0.78 | 22 | MGP |
| 4 | 89 | 0.45 | 0.80 | 17 | MGP |
| 5 | 89 | 0.44 | 0.79 | 16 | MGP |
Interfaces
3 interfaces between chains.
- A–D · 370 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 365 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 337 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GKJ · Translation initiation factor 4E in complex with trinucleotide mRNA 5' cap (m7GpppApG) · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.98
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 6GKJ · PDBe 6GKJ · UniProt P63073
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