Research workbench
Crystal structure of human IZUMO1-juno complex (crystal form 3)
Analyse Crystal structure of human IZUMO1-juno complex (crystal form 3) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JKE
- Type
- protein
- Length
- 870 residues
- Chains
- 4
- 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, SO4, CL
- Pockets
- 13 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Izumo sperm-egg fusion protein 1 | protein | 232 | 40% helix, 31% strand | Q8IYV9 |
| B, D | Sperm-egg fusion protein juno | protein | 203 | 35% helix, 10% strand | A6ND01 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- CL · Chloride ion · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.65 | 0.81 | 36 | empty |
| 2 | 297 | 0.65 | 0.81 | 39 | empty |
| 3 | 165 | 0.52 | 0.79 | 34 | empty |
| 4 | 127 | 0.48 | 0.79 | 25 | empty |
| 5 | 103 | 0.45 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1027 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 992 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 991 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 26 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5JKE · Crystal structure of human IZUMO1-JUNO complex (crystal form 3) · 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 0.97
- 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 0.95
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 5JKE · PDBe 5JKE · UniProt Q8IYV9 · UniProt A6ND01
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.