MolNFT v1 · #168114 · protein
NPC1 structure in gdn micelles at pH 5.5, conformation a
6W5T · Npc intracellular cholesterol transporter 1: “NPC1 structure in gdn micelles at pH 5.5, conformation a”. Electron microscopy, 4 ligands (CLR, NAG, MAN), 16 pockets (best druggability 0.89). MolNFT v1 #168114 on GenesisL1: 3D…
- PDB
- 6W5T
- Type
- protein
- Length
- 1,175 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Npc intracellular cholesterol transporter 1
- UniProt
- O15118
- Ligands
- CLR, NAG, MAN, BMA
- Pockets
- 16 · best druggability 0.89
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 | 1175 | 52% helix, 8% strand | O15118 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · chains A
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 871 | 0.89 | 0.90 | 102 | CLR |
| 2 | 335 | 0.79 | 0.89 | 40 | CLR |
| 3 | 77 | 0.75 | 0.97 | 20 | empty |
| 4 | 471 | 0.68 | 0.79 | 51 | empty |
| 5 | 408 | 0.68 | 0.80 | 57 | empty |
Modifications
Observed in the structure: 14 disulfide, 13 glycan (disulfide, N-glycosylation).
Compared structures
- 6W5T · NPC1 structure in GDN micelles at pH 5.5, conformation a · the same entry in another collection · chain A against A, TM-score 1.00
- O15118 · AlphaFold monomer V2.0 prediction for npc intracellular cholesterol transporter 1 (O15118) · a predicted model of the same protein · chain A against A, TM-score 0.90
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 6W5T · PDBe 6W5T · UniProt O15118
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