MolNFT v1 · #168113 · protein
NPC1 structure in gdn micelles at pH 8.0
6W5S · Npc intracellular cholesterol transporter 1: “NPC1 structure in gdn micelles at pH 8.0”. Electron microscopy, 4 ligands (CLR, POV, NAG), 16 pockets (best druggability 0.87). MolNFT v1 #168113 on GenesisL1: 3D structure, binding…
- PDB
- 6W5S
- Type
- protein
- Length
- 1,194 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npc intracellular cholesterol transporter 1
- UniProt
- O15118
- Ligands
- CLR, POV, NAG, MAN
- Pockets
- 16 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 52% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Npc intracellular cholesterol transporter 1 | protein | 1194 | 52% helix, 8% strand | O15118 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1118 | 0.87 | 0.88 | 103 | empty |
| 2 | 300 | 0.78 | 0.89 | 37 | CLR |
| 3 | 303 | 0.64 | 0.80 | 34 | empty |
| 4 | 347 | 0.61 | 0.78 | 35 | empty |
| 5 | 155 | 0.53 | 0.80 | 24 | empty |
Modifications
Observed in the structure: 15 disulfide, 13 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 O15118
- Elsewhere: RCSB PDB 6W5S · PDBe 6W5S · UniProt O15118
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