Research workbench
Translation initiation factor 4E in complex with 3-MEBN7GPPPG mRNA 5' cap analog
Analyse Translation initiation factor 4E in complex with 3-MEBN7GPPPG mRNA 5' cap analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLT
- Type
- protein
- Length
- 726 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- P3E
- Pockets
- 6 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 34% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 180 | 33% helix, 32% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 183 | 35% helix, 31% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 181 | 34% helix, 31% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 182 | 33% helix, 31% strand | P63073 |
Ligands and binding sites
- P3E · [[(2~{R},3~{S},4~{R},5~{R})-5-[2-azanyl-7-[(3-methylphenyl)methyl]-6-oxidanylidene-1~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl) oxolan-2-yl]methoxy-oxidanyl-phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 153 | 0.50 | 0.78 | 19 | empty |
| 2 | 138 | 0.50 | 0.79 | 22 | empty |
| 3 | 132 | 0.50 | 0.79 | 19 | P3E |
| 4 | 178 | 0.47 | 0.75 | 22 | P3E |
| 5 | 156 | 0.47 | 0.77 | 23 | empty |
Interfaces
3 interfaces between chains.
- B–C · 393 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 361 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 357 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6YLT · Translation initiation factor 4E in complex with 3-MeBn7GpppG mRNA 5' cap analog · 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 C 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 6YLT · PDBe 6YLT · UniProt P63073
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