MolNFT v1 · #118517 · protein
Crystal structure of the human sperm IZUMO1 and egg juno complex
5F4E · Izumo sperm-egg fusion protein 1: “Crystal structure of the human sperm IZUMO1 and egg juno complex”. X-ray diffraction, 2 ligands (NAG, CL), 3 pockets (best druggability 0.67). MolNFT v1 #118517 on GenesisL1: 3D structure, binding…
- PDB
- 5F4E
- Type
- protein
- Length
- 442 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Izumo sperm-egg fusion protein 1; Sperm-egg fusion protein juno
- UniProt
- Q8IYV9, A6ND01
- Ligands
- NAG, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Izumo sperm-egg fusion protein 1 | protein | 233 | 39% helix, 29% strand | Q8IYV9 |
| B | Sperm-egg fusion protein juno | protein | 209 | 28% helix, 10% strand | A6ND01 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · chains B
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 | 276 | 0.67 | 0.83 | 41 | GOL |
| 2 | 212 | 0.52 | 0.77 | 44 | empty |
| 3 | 86 | 0.44 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 961 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 5F4E · Crystal structure of the human sperm Izumo1 and egg Juno complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IYV9 · AlphaFold monomer V2.0 prediction for izumo sperm-egg fusion protein 1 (Q8IYV9) · a predicted model of the same protein · chain A against A, TM-score 0.96
- A6ND01 · AlphaFold monomer V2.0 prediction for sperm-egg fusion protein juno (A6ND01) · a predicted model of the same protein · chain B against A, TM-score 0.92
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 Q8IYV9
- Every structure of UniProt A6ND01
- Elsewhere: RCSB PDB 5F4E · PDBe 5F4E · UniProt Q8IYV9 · UniProt A6ND01
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