Research workbench
Translation initiation factor 4E in complex with M2(7,2'O)GPPCCL2PPG mRNA 5' cap analog
Analyse Translation initiation factor 4E in complex with M2(7,2'O)GPPCCL2PPG mRNA 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J5Y
- Type
- protein
- Length
- 680 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- 6G6
- Pockets
- 7 · best druggability 0.57
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 182 | 31% helix, 29% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 181 | 31% helix, 29% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 155 | 30% helix, 32% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 162 | 33% helix, 27% strand | P63073 |
Ligands and binding sites
- 6G6 · 2-amino-9-{5-O-[(R)-{[(S)-{dichloro[(R)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]-2-O-methyl-beta-D-ribofuranosyl}-7-methyl-9H-purin-7-ium-6-olate · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.57 | 0.81 | 27 | empty |
| 2 | 100 | 0.46 | 0.80 | 17 | empty |
| 3 | 109 | 0.45 | 0.79 | 14 | empty |
| 4 | 113 | 0.44 | 0.78 | 18 | 6G6 |
| 5 | 81 | 0.43 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–C · 429 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 362 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 351 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5J5Y · Translation initiation factor 4E in complex with m2(7,2'O)GppCCl2ppG 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 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 P63073
- Elsewhere: RCSB PDB 5J5Y · PDBe 5J5Y · UniProt P63073
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