MolNFT v1 · #122973 · protein
Translation initiation factor 4E in complex with M7GPPPPG mRNA 5' cap analog
5J5O · Eukaryotic translation initiation factor 4E: “Translation initiation factor 4E in complex with M7GPPPPG mRNA 5' cap analog”. X-ray diffraction, 1 ligand (6G0), 7 pockets (best druggability 0.67). MolNFT v1 #122973 on GenesisL1: 3D…
- 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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