Research workbench
Zp-N domain of mammalian sperm receptor ZP3 (crystal form III)
Analyse Zp-N domain of mammalian sperm receptor ZP3 (crystal form III) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EF7
- Type
- protein
- Length
- 934 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic protein, linker, zona pellucida protein 3
- UniProt
- P0AEX9, P10761
- Ligands
- GLC, ZN, CA
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Maltose-binding periplasmic protein, linker, zona pellucida protein 3 | protein | 467 | 38% helix, 27% strand | P0AEX9, P10761 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- ZN · Zinc ion · metal · 13 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.84 | 0.85 | 110 | GLC |
| 2 | 384 | 0.77 | 0.87 | 46 | GLC |
| 3 | 136 | 0.45 | 0.77 | 22 | empty |
| 4 | 70 | 0.42 | 0.80 | 16 | empty |
| 5 | 83 | 0.41 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 951 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3EF7 · ZP-N domain of mammalian sperm receptor ZP3 (crystal form III) · the same entry in another collection · chain A against A, TM-score 1.00
- P10761 · AlphaFold monomer V2.0 prediction for zona pellucida sperm-binding protein 3 (P10761) · a predicted model of the same protein · chain A against A, TM-score 0.20
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 P0AEX9
- Every structure of UniProt P10761
- Elsewhere: RCSB PDB 3EF7 · PDBe 3EF7 · UniProt P0AEX9 · UniProt P10761
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