Research workbench
Zp-N domain of mammalian sperm receptor ZP3 (crystal form I)
Analyse Zp-N domain of mammalian sperm receptor ZP3 (crystal form I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4C
- Type
- protein
- Length
- 470 residues
- Chains
- 1
- 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, CD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Maltose-binding periplasmic protein, linker, zona pellucida protein 3 | protein | 470 | 36% helix, 26% strand | P0AEX9, P10761 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- CD · Cadmium ion · metal · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1020 | 0.79 | 0.81 | 75 | GLC |
| 2 | 58 | 0.42 | 0.82 | 18 | empty |
| 3 | 59 | 0.40 | 0.80 | 15 | empty |
| 4 | 67 | 0.31 | 0.74 | 17 | empty |
| 5 | 59 | 0.31 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3D4C · ZP-N domain of mammalian sperm receptor ZP3 (crystal form I) · 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 3D4C · PDBe 3D4C · UniProt P0AEX9 · UniProt P10761
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