Research workbench
Stapled-peptides tailored against initiation of translation
Analyse Stapled-peptides tailored against initiation of translation in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZK9
- 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; ACE-arg-ile-ile-tyr-ser-arg-MK8-gln-leu-leu-M…
- UniProt
- P06730
- Ligands
- ACE, MGP, NH2
- Pockets
- 1 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 183 | 33% helix, 28% strand | P06730 |
| B | ACE-arg-ile-ile-tyr-ser-arg-MK8-gln-leu-leu-MK8-leu-lys- NH2 | protein | 13 | 46% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A, B
- MGP · 7-methyl-guanosine-5'-triphosphate · ligand · chains A
- NH2 · Amino group · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
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 | 112 | 0.47 | 0.79 | 20 | MGP |
Interfaces
1 interface between chains.
- A–B · 675 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (nonstandard, covalent ligand).
Compared structures
- 5ZK9 · 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
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
- Elsewhere: RCSB PDB 5ZK9 · PDBe 5ZK9 · UniProt P06730
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