Research workbench
Translation initiation factor 4E in complex with M7GPPPPG mRNA 5' cap analog
Analyse Translation initiation factor 4E in complex with M7GPPPPG 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
- 5J5O
- Type
- protein
- Length
- 720 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- 6G0
- Pockets
- 7 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Eukaryotic translation initiation factor 4E | protein | 181 | 31% helix, 29% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 179 | 33% helix, 30% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 179 | 35% helix, 28% strand | P63073 |
Ligands and binding sites
- 6G0 · 5'-O-[(R)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]-7-methylguanosine · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.67 | 0.85 | 35 | empty |
| 2 | 159 | 0.51 | 0.78 | 24 | empty |
| 3 | 116 | 0.50 | 0.80 | 19 | empty |
| 4 | 94 | 0.46 | 0.80 | 19 | empty |
| 5 | 68 | 0.44 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 431 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 368 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5J5O · Translation initiation factor 4E in complex with m7GppppG mRNA 5' cap analog · the same entry in another collection · chain A against A, 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 5J5O · PDBe 5J5O · UniProt P63073
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