MolNFT v1 · #135711 · protein

Structure of human niemann-pick C1 protein

5U74: “Structure of human niemann-pick C1 protein”. X-ray diffraction, 2 ligands (NAG, MAN), 9 pockets (best druggability 0.88). MolNFT v1 #135711 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5U74
Type: protein
Length: 900 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Niemann-pick C1 protein
UniProt: O15118
Ligands: NAG, MAN
Pockets: 9 · best druggability 0.88

Structure

x-ray diffraction · 1 distinct chain · 55% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Niemann-pick C1 protein	protein	900	55% helix, 7% strand	O15118

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A
MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A

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

Pockets

9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1191	0.88	0.89	101	MES
2	190	0.52	0.78	21	empty
3	107	0.50	0.81	19	empty
4	68	0.43	0.81	20	empty
5	87	0.35	0.74	17	empty

Modifications

Observed in the structure: 12 glycan, 6 disulfide (N-glycosylation, disulfide, glycosylation).

Compared structures

5U74 · Structure of human Niemann-Pick C1 protein · 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 0.94

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 5U74 · PDBe 5U74 · UniProt O15118

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