Research workbench
Molecular basis of egg coat filament cross-linking: zn-sad structure of the partially deglycosylated ZP1 zp-N1 domain homodimer
Analyse Molecular basis of egg coat filament cross-linking: zn-sad structure of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GF7
- Type
- protein
- Length
- 208 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Zona pellucida sperm-binding protein 1,ZONA pellucida sperm-binding protein 1
- UniProt
- A0A140JXP0
- Ligands
- NAG, ZN
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 0% helix, 58% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Zona pellucida sperm-binding protein 1,ZONA pellucida sperm-binding protein 1 | protein | 105 | 0% helix, 57% strand | A0A140JXP0 |
| B | Zona pellucida sperm-binding protein 1,ZONA pellucida sperm-binding protein 1 | protein | 103 | 0% helix, 58% strand | A0A140JXP0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- ZN · Zinc ion · metal · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 136 | 0.68 | 0.89 | 22 | empty |
| 2 | 73 | 0.38 | 0.78 | 18 | ZN |
| 3 | 50 | 0.26 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 640 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6GF7 · Molecular basis of egg coat filament cross-linking: Zn-SAD structure of the partially… · the same entry in another collection · 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 A0A140JXP0
- Elsewhere: RCSB PDB 6GF7 · PDBe 6GF7 · UniProt A0A140JXP0
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