Research workbench
Crystal structure of the human 4EHP-4E-BP1 complex
Analyse Crystal structure of the human 4EHP-4E-BP1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NVN
- Type
- protein
- Length
- 400 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E type 2; Eukaryotic translation initiation…
- UniProt
- O60573, Q13541
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E type 2 | protein | 165 | 27% helix, 35% strand | O60573 |
| B | Eukaryotic translation initiation factor 4E-binding protein 1 | protein | 34 | 32% helix, 3% strand | Q13541 |
| C | Eukaryotic translation initiation factor 4E type 2 | protein | 166 | 25% helix, 33% strand | O60573 |
| D | Eukaryotic translation initiation factor 4E-binding protein 1 | protein | 35 | 37% helix, 3% strand | Q13541 |
Ligands and binding sites
- FMT · Formic acid · additive · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.61 | 0.79 | 44 | FMT |
| 2 | 284 | 0.55 | 0.76 | 31 | empty |
| 3 | 191 | 0.47 | 0.75 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1423 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1354 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 647 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 188 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5NVN · Crystal structure of the human 4EHP-4E-BP1 complex · the same entry in another collection · chain D against D, TM-score 1.00
- O60573 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E type 2… · a predicted model of the same protein · chain C against A, TM-score 0.95
- Q13541 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 4E-binding… · a predicted model of the same protein · chain D against A, TM-score 0.86
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 O60573
- Every structure of UniProt Q13541
- Elsewhere: RCSB PDB 5NVN · PDBe 5NVN · UniProt O60573 · UniProt Q13541
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