Research workbench
Complex of C. elegans EIF4E-3 with the 4E-binding protein mextli
Analyse Complex of C. elegans EIF4E-3 with the 4E-binding protein mextli in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ABY
- Type
- protein
- Length
- 655 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E-3; 4E-binding protein mextli
- UniProt
- O61955, Q9XW13
- Ligands
- MG
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E-3 | protein | 179 | 31% helix, 30% strand | O61955 |
| B, D | 4E-binding protein mextli | protein | 39 | 56% helix, 3% strand | Q9XW13 |
| C | Eukaryotic translation initiation factor 4E-3 | protein | 181 | 31% helix, 30% strand | O61955 |
| E | Eukaryotic translation initiation factor 4E-3 | protein | 178 | 31% helix, 30% strand | O61955 |
| F | 4E-binding protein mextli | protein | 39 | 56% helix, 3% strand | Q9XW13 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains C
- GOL · Glycerol · additive · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.65 | 0.75 | 65 | empty |
| 2 | 154 | 0.63 | 0.86 | 23 | empty |
| 3 | 347 | 0.62 | 0.78 | 35 | empty |
| 4 | 114 | 0.41 | 0.76 | 16 | GOL, MG |
| 5 | 119 | 0.39 | 0.75 | 17 | GOL |
Interfaces
10 interfaces between chains.
- E–F · 1398 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1364 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1362 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 341 Ų buried · 4 hydrogen bonds · protein-protein
- C–E · 331 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5ABY · Complex of C. elegans eIF4E-3 with the 4E-binding protein Mextli · the same entry in another collection · chain F against F, TM-score 1.00
- O61955 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-3… · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q9XW13 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain B against A, TM-score 0.42
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 O61955
- Every structure of UniProt Q9XW13
- Elsewhere: RCSB PDB 5ABY · PDBe 5ABY · UniProt O61955 · UniProt Q9XW13
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