Research workbench
Zp-N domain of mammalian sperm receptor ZP3 (crystal form II)
Analyse Zp-N domain of mammalian sperm receptor ZP3 (crystal form II) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D4G
- Type
- protein
- Length
- 3,767 residues
- Chains
- 8
- 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, CA
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Maltose-binding periplasmic protein, linker, zona pellucida protein 3 | protein | 471 | 38% helix, 27% strand | P0AEX9, P10761 |
| D, H | Maltose-binding periplasmic protein, linker, zona pellucida protein 3 | protein | 469 | 38% helix, 27% strand | P0AEX9, P10761 |
| E, F, G | Maltose-binding periplasmic protein, linker, zona pellucida protein 3 | protein | 472 | 38% helix, 27% strand | P0AEX9, P10761 |
Ligands and binding sites
- GLC · alpha-D-glucopyranose · sugar · 16 copies · chains A, B, C, D, E, F, G, H
- CA · Calcium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 939 | 0.89 | 0.91 | 122 | GLC, CA |
| 2 | 868 | 0.86 | 0.88 | 84 | GLC, CA |
| 3 | 969 | 0.86 | 0.87 | 96 | GLC, CA |
| 4 | 1037 | 0.81 | 0.82 | 93 | GLC, CA |
| 5 | 1073 | 0.81 | 0.82 | 95 | GLC, CA |
Interfaces
7 interfaces between chains.
- B–C · 1022 Ų buried · 3 hydrogen bonds · protein-protein
- F–H · 1017 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 646 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 605 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3D4G · ZP-N domain of mammalian sperm receptor ZP3 (crystal form II) · the same entry in another collection · chain G against G, 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 E 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 3D4G · PDBe 3D4G · UniProt P0AEX9 · UniProt P10761
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