MolNFT v1 · #168112 · protein

NPC1 structure in nanodisc

6W5R · Npc intracellular cholesterol transporter 1: “NPC1 structure in nanodisc”. Electron microscopy, 4 ligands (CLR, NAG, BMA), 15 pockets (best druggability 0.87). MolNFT v1 #168112 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6W5R
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, NAG, BMA, MAN
Pockets: 15 · best druggability 0.87

Structure

electron microscopy · 1 distinct chain · 50% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Npc intracellular cholesterol transporter 1	protein	1194	50% helix, 8% strand	O15118

Ligands and binding sites

CLR · Cholesterol · ligand · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 17 copies · chains A
BMA · beta-D-mannopyranose · sugar · chains A
MAN · alpha-D-mannopyranose · sugar

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

Pockets

15 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	1150	0.87	0.88	111	empty
2	387	0.82	0.91	33	CLR
3	61	0.71	0.97	21	empty
4	485	0.68	0.79	49	empty
5	525	0.63	0.76	44	empty

Modifications

Observed in the structure: 15 disulfide, 13 glycan (disulfide, N-glycosylation).

Compared structures

6W5R · NPC1 structure in Nanodisc · 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 6W5R · PDBe 6W5R · UniProt O15118

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