Research workbench
Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA 5' cap diastereomer 1 (M7GPPSPAPG D1)
Analyse Translation initiation factor 4E in complex with beta-phosphorothioate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GKK
- Type
- protein
- Length
- 723 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- WZO
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 182 | 36% helix, 30% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 184 | 34% helix, 31% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 179 | 31% helix, 29% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 178 | 31% helix, 29% strand | P63073 |
Ligands and binding sites
- WZO · [(2~{R},3~{R},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1~{H}-purin-7-ium-9-yl)-4-methoxy-3-oxidanyl-oxolan-2-yl]methyl [phosphonooxy(sulfanyl) phosphoryl] hydrogen phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.52 | 0.87 | 24 | empty |
| 2 | 177 | 0.49 | 0.76 | 22 | empty |
| 3 | 103 | 0.48 | 0.80 | 22 | WZO |
| 4 | 93 | 0.44 | 0.79 | 18 | empty |
| 5 | 103 | 0.44 | 0.78 | 17 | WZO |
Interfaces
3 interfaces between chains.
- B–D · 381 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 376 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 349 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6GKK · Translation initiation factor 4E in complex with beta-phosphorothioate trinucleotide mRNA… · 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 D 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 P63073
- Elsewhere: RCSB PDB 6GKK · PDBe 6GKK · UniProt P63073
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