Research workbench
Crystal structure of S. cerevisia niemann-pick type C protein NCR1
Analyse Crystal structure of S. cerevisia niemann-pick type C protein NCR1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R4L
- Type
- protein
- Length
- 1,096 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npc intracellular cholesterol transporter 1-related protein 1
- UniProt
- Q12200
- Ligands
- ERG, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npc intracellular cholesterol transporter 1-related protein 1 | protein | 1096 | 50% helix, 6% strand | Q12200 |
Ligands and binding sites
- ERG · Ergosterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.86 | 0.90 | 80 | ERG |
| 2 | 480 | 0.81 | 0.87 | 63 | empty |
| 3 | 239 | 0.78 | 0.91 | 45 | empty |
| 4 | 90 | 0.77 | 0.98 | 22 | empty |
| 5 | 156 | 0.71 | 0.90 | 23 | empty |
Modifications
Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6R4L · Crystal structure of S. cerevisia Niemann-Pick type C protein NCR1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q12200 · AlphaFold monomer V2.0 prediction for npc intracellular sterol transporter 1-related… · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q12200
- Elsewhere: RCSB PDB 6R4L · PDBe 6R4L · UniProt Q12200
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