Research workbench
Crystal structure of the gamma-secretase component nicastrin
Analyse Crystal structure of the gamma-secretase component nicastrin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R12
- Type
- protein
- Length
- 573 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative uncharacterized protein
- UniProt
- F0ZBA6
- Ligands
- NAG, BMA, CA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative uncharacterized protein | protein | 573 | 27% helix, 27% strand | F0ZBA6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.57 | 0.75 | 56 | CA |
| 2 | 159 | 0.52 | 0.79 | 20 | empty |
| 3 | 243 | 0.51 | 0.75 | 29 | empty |
| 4 | 146 | 0.48 | 0.77 | 23 | empty |
| 5 | 93 | 0.37 | 0.75 | 15 | empty |
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
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 F0ZBA6
- Elsewhere: RCSB PDB 4R12 · PDBe 4R12 · UniProt F0ZBA6
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