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
- 5ZK7
- Type
- protein
- Length
- 377 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E; ACE-arg-tyr-ser-arg-MK8-gln-leu-leu-MK8-leu-p…
- UniProt
- P06730
- Ligands
- ACE, MGT, IOD, NH2, CL
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 178 | 34% helix, 30% strand | P06730 |
| B | Eukaryotic translation initiation factor 4E | protein | 175 | 33% helix, 29% strand | P06730 |
| C, D | ACE-arg-tyr-ser-arg-MK8-gln-leu-leu-MK8-leu-phe-arg-NH2 | protein | 12 | 50% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, C, D
- MGT · 7N-methyl-8-hydroguanosine-5'-triphosphate · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 5 copies · chains A, B, C, D
- NH2 · Amino group · ion · 2 copies · chains A, C, B, D
- CL · Chloride ion · ion · chains A, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 114 | 0.61 | 0.86 | 26 | GOL |
| 2 | 229 | 0.54 | 0.77 | 34 | IOD |
| 3 | 131 | 0.46 | 0.77 | 18 | empty |
| 4 | 90 | 0.44 | 0.79 | 16 | MGT |
| 5 | 93 | 0.42 | 0.78 | 17 | MGT |
Interfaces
6 interfaces between chains.
- A–D · 645 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 591 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 434 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 320 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 191 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 5ZK7 · 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 B 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 P06730
- Elsewhere: RCSB PDB 5ZK7 · PDBe 5ZK7 · UniProt P06730
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