Research workbench

NPC1D(NTD):25HYDROXYCHOLESTEROL

Analyse NPC1D(NTD):25HYDROXYCHOLESTEROL in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3GKJ
Type: protein
Length: 225 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Niemann-pick C1 protein
UniProt: O15118
Ligands: HC3, NAG
Pockets: 1 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Niemann-pick C1 protein	protein	225	36% helix, 24% strand	O15118

Ligands and binding sites

HC3 · 25-hydroxycholesterol · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	296	0.78	0.89	31	HC3

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

3GKJ · NPC1D(NTD):25hydroxycholesterol · 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 0.98

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 O15118
Elsewhere: RCSB PDB 3GKJ · PDBe 3GKJ · UniProt O15118

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