MolNFT v1 · #141820 · protein
Stapled-peptides tailored against initiation of translation
5ZK5 · Eukaryotic translation initiation factor 4E: “Stapled-peptides tailored against initiation of translation”. X-ray diffraction, 2 ligands (MGT, NH2), 1 pocket (best druggability 0.41). MolNFT v1 #141820 on GenesisL1: 3D structure…
- PDB
- 5ZK5
- Type
- protein
- Length
- 196 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E; Lys-arg-tyr-ser-arg-glu-gln-leu-leu-MK8-phe-g…
- UniProt
- P06730, Q04637
- Ligands
- MGT, NH2
- Pockets
- 1 · best druggability 0.41
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 182 | 34% helix, 28% strand | P06730 |
| B | Lys-arg-tyr-ser-arg-glu-gln-leu-leu-MK8-phe-gln-arg-MK8 | protein | 14 | 64% helix, 0% strand | Q04637 |
Ligands and binding sites
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · chains A
- NH2 · Amino group · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.41 | 0.78 | 16 | MGT |
Interfaces
1 interface between chains.
- A–B · 629 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5ZK5 · Stapled-peptides tailored against initiation of translation · the same entry in another collection · chain A against A, 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 0.98
- Q04637 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4 gamma 1… · a predicted model of the same protein · chain B against A, TM-score 0.53
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 Q04637
- Elsewhere: RCSB PDB 5ZK5 · PDBe 5ZK5 · UniProt P06730 · UniProt Q04637
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