Research workbench
Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences
Analyse Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5NVM
- Type
- protein
- Length
- 407 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Eukaryotic translation initiation factor 4E type 2; GRB10-interacting gyf protein 2
- UniProt
- O60573, Q6Y7W6
- Ligands
- PO4
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Eukaryotic translation initiation factor 4E type 2 | protein | 176 | 24% helix, 35% strand | O60573 |
| B, D | GRB10-interacting gyf protein 2 | protein | 37 | 41% helix, 3% strand | Q6Y7W6 |
| C | Eukaryotic translation initiation factor 4E type 2 | protein | 157 | 25% helix, 37% strand | O60573 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 277 | 0.62 | 0.80 | 29 | empty |
| 2 | 201 | 0.47 | 0.75 | 28 | empty |
| 3 | 138 | 0.44 | 0.76 | 26 | empty |
| 4 | 70 | 0.30 | 0.74 | 17 | empty |
| 5 | 56 | 0.27 | 0.74 | 10 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1461 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1455 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 363 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 202 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 187 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5NVM · Crystal structure of the human 4EHP-GIGYF2 complex lacking the auxiliary sequences · 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 0.97
- Q6Y7W6 · AlphaFold monomer V2.0 prediction for GRB10-interacting gyf protein 2 (Q6Y7W6) · a predicted model of the same protein · chain B against A, TM-score 0.63
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 Q6Y7W6
- Elsewhere: RCSB PDB 5NVM · PDBe 5NVM · UniProt O60573 · UniProt Q6Y7W6
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