MolNFT v1 · #118525 · protein
Crystal structure of the human egg surface protein juno
5F4Q · Sperm-egg fusion protein juno: “Crystal structure of the human egg surface protein juno”. X-ray diffraction, 2 ligands (NAG, CL), 7 pockets (best druggability 0.69). MolNFT v1 #118525 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5F4Q
- Type
- protein
- Length
- 790 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sperm-egg fusion protein juno
- UniProt
- A6ND01
- Ligands
- NAG, CL
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sperm-egg fusion protein juno | protein | 197 | 33% helix, 11% strand | A6ND01 |
| B | Sperm-egg fusion protein juno | protein | 201 | 32% helix, 10% strand | A6ND01 |
| C | Sperm-egg fusion protein juno | protein | 195 | 33% helix, 11% strand | A6ND01 |
| D | Sperm-egg fusion protein juno | protein | 197 | 34% helix, 12% strand | A6ND01 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 3 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 593 | 0.69 | 0.78 | 57 | empty |
| 2 | 579 | 0.67 | 0.77 | 56 | GOL |
| 3 | 299 | 0.65 | 0.81 | 35 | GOL |
| 4 | 263 | 0.65 | 0.82 | 35 | GOL |
| 5 | 280 | 0.49 | 0.73 | 41 | empty |
Interfaces
5 interfaces between chains.
- B–D · 518 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 306 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 235 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 127 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 12 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 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 A6ND01
- Elsewhere: RCSB PDB 5F4Q · PDBe 5F4Q · UniProt A6ND01
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