Research workbench
Crystal structure of mouse sperm C-type lysozyme-like protein 1
Analyse Crystal structure of mouse sperm C-type lysozyme-like protein 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YF2
- Type
- protein
- Length
- 386 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sperm acrosome membrane-associated protein 3
- UniProt
- Q9D9X8
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sperm acrosome membrane-associated protein 3 | protein | 130 | 42% helix, 9% strand | Q9D9X8 |
| B | Sperm acrosome membrane-associated protein 3 | protein | 129 | 41% helix, 9% strand | Q9D9X8 |
| C | Sperm acrosome membrane-associated protein 3 | protein | 127 | 43% helix, 9% strand | Q9D9X8 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.46 | 0.80 | 19 | empty |
| 2 | 105 | 0.39 | 0.76 | 17 | empty |
| 3 | 86 | 0.34 | 0.74 | 17 | empty |
| 4 | 51 | 0.24 | 0.73 | 12 | empty |
| 5 | 55 | 0.23 | 0.71 | 12 | empty |
Interfaces
2 interfaces between chains.
- B–C · 795 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 4YF2 · Crystal structure of mouse sperm C-type lysozyme-like protein 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D9X8 · AlphaFold monomer V2.0 prediction for sperm acrosome membrane- associated protein 3… · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q9D9X8
- Elsewhere: RCSB PDB 4YF2 · PDBe 4YF2 · UniProt Q9D9X8
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