MolNFT v1 · #51485 · protein
Crystallographic and mass spectrometric characterisation of EIF4E with N7-cap derivatives
2V8X · Eukaryotic translation initiation factor 4E: “Crystallographic and mass spectrometric characterisation of EIF4E with N7-cap derivatives”. X-ray diffraction, 1 ligand (MGQ), 3 pockets (best druggability 0.47). MolNFT v1 #51485 on…
- PDB
- 2V8X
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E; Eukaryotic translation initiation factor…
- UniProt
- P06730, Q13541
- Ligands
- MGQ
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 181 | 32% helix, 29% strand | P06730 |
| B, F | Eukaryotic translation initiation factor 4E-binding protein 1 | protein | 14 | 43% helix, 0% strand | Q13541 |
| E | Eukaryotic translation initiation factor 4E | protein | 179 | 28% helix, 30% strand | P06730 |
Ligands and binding sites
- MGQ · 7-benzyl guanine monophosphate · ligand · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.47 | 0.78 | 19 | MGQ |
| 2 | 99 | 0.45 | 0.79 | 18 | MGQ |
| 3 | 127 | 0.44 | 0.77 | 25 | empty |
Interfaces
4 interfaces between chains.
- E–F · 771 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 703 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 461 Ų buried · 7 hydrogen bonds · protein-protein
- A–F · 131 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2V8X · Crystallographic and mass spectrometric characterisation of eIF4E with N7-cap derivatives · the same entry in another collection · chain F against F, TM-score 1.00
- P06730 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E (P06730) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain F against A, TM-score 0.69
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 P06730
- Every structure of UniProt Q13541
- Elsewhere: RCSB PDB 2V8X · PDBe 2V8X · UniProt P06730 · UniProt Q13541
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