Research workbench
Crystal structure of the human 4EHP-GIGYF1 complex
Analyse Crystal structure of the human 4EHP-GIGYF1 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NVK
- Type
- protein
- Length
- 955 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E type 2; GRB10-interacting gyf protein 1
- UniProt
- O60573, O75420
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 7 distinct chains · 30% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E type 2 | protein | 172 | 25% helix, 32% strand | O60573 |
| B | GRB10-interacting gyf protein 1 | protein | 68 | 43% helix, 3% strand | O75420 |
| C, E | Eukaryotic translation initiation factor 4E type 2 | protein | 168 | 23% helix, 32% strand | O60573 |
| D | GRB10-interacting gyf protein 1 | protein | 74 | 34% helix, 4% strand | O75420 |
| F | GRB10-interacting gyf protein 1 | protein | 67 | 40% helix, 3% strand | O75420 |
| G | Eukaryotic translation initiation factor 4E type 2 | protein | 172 | 25% helix, 33% strand | O60573 |
| H | GRB10-interacting gyf protein 1 | protein | 66 | 44% helix, 3% strand | O75420 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.85 | 0.87 | 79 | empty |
| 2 | 1028 | 0.84 | 0.85 | 93 | empty |
| 3 | 246 | 0.54 | 0.77 | 24 | empty |
| 4 | 217 | 0.54 | 0.78 | 33 | empty |
| 5 | 228 | 0.52 | 0.77 | 29 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2270 Ų buried · 32 hydrogen bonds · protein-protein
- G–H · 2257 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2216 Ų buried · 34 hydrogen bonds · protein-protein
- E–F · 2161 Ų buried · 34 hydrogen bonds · protein-protein
- A–D · 661 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5NVK · Crystal structure of the human 4EHP-GIGYF1 complex · the same entry in another collection · chain H against H, 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 A against A, TM-score 0.94
- O75420 · AlphaFold monomer V2.0 prediction for GRB10-interacting gyf protein 1 (O75420) · a predicted model of the same protein · chain H against A, TM-score 0.54
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 O75420
- Elsewhere: RCSB PDB 5NVK · PDBe 5NVK · UniProt O60573 · UniProt O75420
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