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Structure of human NPC1L1

Analyse Structure of human NPC1L1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N4U
Type: protein
Length: 1,906 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Isoform 2 of NPC1-like intracellular cholesterol transporter 1
UniProt: Q9UHC9
Ligands: CLR, VIV, POV, NAG
Pockets: 16 · best druggability 0.88

Structure

electron microscopy · 1 distinct chain · 55% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Isoform 2 of NPC1-like intracellular cholesterol transporter 1	protein	953	55% helix, 8% strand	Q9UHC9

Ligands and binding sites

CLR · Cholesterol · ligand · 4 copies · chains A, B
VIV · (2R)-2,5,7,8-tetramethyl-2-[(4R,8R)-4,8,12-trimethyltridecyl]chroman-6-ol · ligand · 2 copies · chains A, B
POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1077	0.88	0.88	110	VIV
2	1112	0.87	0.88	110	VIV
3	842	0.70	0.75	60	POV
4	462	0.63	0.77	33	empty
5	447	0.61	0.76	34	empty

Interfaces

1 interface between chains.

A–B · 471 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 glycan, 12 disulfide (N-glycosylation, disulfide).

Compared structures

7N4U · Structure of human NPC1L1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHC9 · 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 Q9UHC9
Elsewhere: RCSB PDB 7N4U · PDBe 7N4U · UniProt Q9UHC9

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