Research workbench
Crystal structure of full-length sperm receptor ZP3 at 2.6 a resolution
Analyse Crystal structure of full-length sperm receptor ZP3 at 2.6 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NK3
- Type
- protein
- Length
- 589 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zona pellucida 3
- UniProt
- P79762
- Ligands
- A2G, GAL
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zona pellucida 3 | protein | 284 | 6% helix, 44% strand | P79762 |
| B | Zona pellucida 3 | protein | 270 | 7% helix, 44% strand | P79762 |
| C | Zona pellucida 3 | protein | 21 | 0% helix, 52% strand | P79762 |
| D | Zona pellucida 3 | protein | 14 | 0% helix, 79% strand | P79762 |
Ligands and binding sites
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar
- FLC · Citrate anion · additive · chains A, B, C
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 | 799 | 0.74 | 0.79 | 91 | FLC |
| 2 | 88 | 0.39 | 0.77 | 27 | empty |
| 3 | 117 | 0.38 | 0.74 | 24 | empty |
| 4 | 69 | 0.33 | 0.76 | 16 | empty |
| 5 | 61 | 0.32 | 0.76 | 20 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1289 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 1140 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 1107 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 330 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 71 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 1 glycan (disulfide, O-glycosylation).
Compared structures
- 3NK3 · Crystal structure of full-length sperm receptor ZP3 at 2.6 A resolution · the same entry in another collection · chain D against D, TM-score 1.00
- P79762 · AlphaFold monomer V2.0 prediction for zona pellucida sperm-binding protein 3 (P79762) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 P79762
- Elsewhere: RCSB PDB 3NK3 · PDBe 3NK3 · UniProt P79762
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