Research workbench
Crystal structure of human IZUMO1
Analyse Crystal structure of human IZUMO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JK9
- Type
- protein
- Length
- 1,390 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Izumo sperm-egg fusion protein 1
- UniProt
- Q8IYV9
- Ligands
- NAG
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Izumo sperm-egg fusion protein 1 | protein | 241 | 39% helix, 28% strand | Q8IYV9 |
| B | Izumo sperm-egg fusion protein 1 | protein | 231 | 41% helix, 29% strand | Q8IYV9 |
| C | Izumo sperm-egg fusion protein 1 | protein | 237 | 40% helix, 29% strand | Q8IYV9 |
| D | Izumo sperm-egg fusion protein 1 | protein | 212 | 42% helix, 22% strand | Q8IYV9 |
| E | Izumo sperm-egg fusion protein 1 | protein | 231 | 40% helix, 29% strand | Q8IYV9 |
| F | Izumo sperm-egg fusion protein 1 | protein | 238 | 41% helix, 27% strand | Q8IYV9 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 768 | 0.68 | 0.75 | 56 | empty |
| 2 | 612 | 0.64 | 0.74 | 56 | empty |
| 3 | 314 | 0.58 | 0.77 | 44 | empty |
| 4 | 250 | 0.57 | 0.78 | 37 | empty |
| 5 | 327 | 0.56 | 0.76 | 32 | empty |
Interfaces
7 interfaces between chains.
- C–E · 950 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 945 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 408 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 309 Ų buried · 7 hydrogen bonds · protein-protein
- B–F · 108 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 30 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
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
- Elsewhere: RCSB PDB 5JK9 · PDBe 5JK9 · UniProt Q8IYV9
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