Research workbench
Translation initiation factor 4E in complex with 4-cl-BN7GPPPG mRNA 5' cap analog
Analyse Translation initiation factor 4E in complex with 4-cl-BN7GPPPG mRNA 5' cap… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6YLV
- Type
- protein
- Length
- 725 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E
- UniProt
- P63073
- Ligands
- OYW
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E | protein | 183 | 32% helix, 30% strand | P63073 |
| B | Eukaryotic translation initiation factor 4E | protein | 185 | 31% helix, 30% strand | P63073 |
| C | Eukaryotic translation initiation factor 4E | protein | 179 | 27% helix, 30% strand | P63073 |
| D | Eukaryotic translation initiation factor 4E | protein | 178 | 29% helix, 31% strand | P63073 |
Ligands and binding sites
- OYW · 4-Cl-Bn7GpppG mRNA 5' cap analog · 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
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 | 123 | 0.52 | 0.81 | 21 | OYW |
| 2 | 110 | 0.49 | 0.80 | 18 | OYW |
| 3 | 99 | 0.48 | 0.81 | 20 | OYW |
| 4 | 152 | 0.48 | 0.77 | 25 | empty |
| 5 | 84 | 0.45 | 0.80 | 14 | OYW |
Interfaces
3 interfaces between chains.
- B–C · 449 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 405 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6YLV · Translation initiation factor 4E in complex with 4-Cl-Bn7GpppG 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 6YLV · PDBe 6YLV · UniProt P63073
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