Research workbench
Zp-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in P21221)
Analyse Zp-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OSQ
- Type
- protein
- Length
- 944 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Maltose-binding periplasmic PROTEIN,ZONA pellucida sperm- binding protein 3
- UniProt
- P0AEX9, P10761
- Ligands
- GLC, CA
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic PROTEIN,ZONA pellucida sperm- binding protein 3 | protein | 472 | 39% helix, 27% strand | P0AEX9, P10761 |
| B | Maltose-binding periplasmic PROTEIN,ZONA pellucida sperm- binding protein 3 | protein | 472 | 38% helix, 27% strand | P0AEX9, P10761 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A, B
- CA · Calcium ion · metal · 6 copies · chains A, B
- PGE · Triethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.81 | 0.82 | 82 | GLC |
| 2 | 1102 | 0.80 | 0.82 | 94 | GLC |
| 3 | 219 | 0.65 | 0.83 | 32 | empty |
| 4 | 473 | 0.64 | 0.77 | 49 | CA |
| 5 | 88 | 0.43 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 635 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5OSQ · ZP-N domain of mammalian sperm receptor ZP3 (crystal form II, processed in P21221) · 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 0.24
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 5OSQ · PDBe 5OSQ · UniProt P0AEX9 · UniProt P10761
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