Research workbench
Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1) in complex with an ezetimibe analog
Analyse Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6V3H
- Type
- protein
- Length
- 1,232 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NPC1-like intracellular cholesterol transporter 1
- UniProt
- Q6T3U3
- Ligands
- Y01, QO1, NAG
- Pockets
- 11 · best druggability 0.90
Structure
electron microscopy · 1 distinct chain · 53% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NPC1-like intracellular cholesterol transporter 1 | protein | 1232 | 53% helix, 12% strand | Q6T3U3 |
Ligands and binding sites
- Y01 · Cholesterol hemisuccinate · ligand · 2 copies · chains A
- QO1 · 4-[(2S,3R)-3-[(3S)-3-(4-fluorophenyl)-3-hydroxypropyl]-1-(4-{3-[(methylsulfonyl)amino]prop-1-yn-1-yl}phenyl)-4-oxoazetidin-2-yl]phenyl beta-D-glucopyranosiduronic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 878 | 0.90 | 0.93 | 131 | QO1 |
| 2 | 390 | 0.73 | 0.84 | 52 | empty |
| 3 | 153 | 0.61 | 0.84 | 37 | empty |
| 4 | 404 | 0.61 | 0.76 | 29 | empty |
| 5 | 277 | 0.60 | 0.79 | 40 | empty |
Modifications
Observed in the structure: 14 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 6V3H · Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1) in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6T3U3 · AlphaFold monomer V2.0 prediction for NPC1-like intracellular cholesterol transporter 1… · a predicted model of the same protein · chain A 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 Q6T3U3
- Elsewhere: RCSB PDB 6V3H · PDBe 6V3H · UniProt Q6T3U3
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