SMTL ID : 6v3h.1

Structure of NPC1-like intracellular cholesterol transporter 1 (NPC1L1) in complex with an ezetimibe analog

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

6 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 3 residues within 4Å: Chain A: N.118, T.120, P.210 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.224, E.225 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.477, T.479, L.480 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain A: N.889, S.892 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: E.379, H.380, N.1018, I.1026 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: I.246, N.1056, A.1059, D.1060 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.246

6 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.7: 4 residues within 4Å: Chain A: E.17, G.19, K.20, N.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.20, A:N.33 NAG.8: 1 residues within 4Å: Chain A: N.444 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.486 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.486 NAG.10: 2 residues within 4Å: Chain A: R.430, N.586 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: E.893, A.894, N.897, G.904, P.981 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.893, A:A.894 Hydrogen bonds: A:N.897 NAG.12: 1 residues within 4Å: Chain A: N.976 No protein-ligand interaction detected (PLIP)

2 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.13: 9 residues within 4Å: Chain A: I.353, I.610, L.613, A.617, Y.620, L.657, L.661, M.664, F.684 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.353, A:I.610, A:L.613, A:A.617, A:Y.620, A:L.657, A:L.661, A:F.684 Y01.14: 4 residues within 4Å: Chain A: L.1136, W.1140, L.1226, L.1230 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.1136, A:L.1226, A:L.1230

1 x 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(Non-covalent)

QO1.15: 20 residues within 4Å: Chain A: I.85, T.86, L.89, I.157, A.159, A.160, S.167, M.168, L.193, P.454, L.455, L.510, F.512, M.523, G.527, A.528, P.1001, N.1002, P.1006, A.1011 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.160, A:L.510, A:F.512, A:A.528, A:P.1001, A:P.1001, A:P.1006 Hydrogen bonds: A:P.1001 pi-Stacking: A:F.512

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C.S. et al., Cryo-EM structures of NPC1L1 reveal mechanisms of cholesterol transport and ezetimibe inhibition. Sci Adv (2020)

Release Date

2020-07-01

Peptides

NPC1-like intracellular cholesterol transporter 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Membrane

We predict this structure to be a membrane protein.
Show / Hide

NPC1-like intracellular cholesterol transporter 1

Related Entries With Identical Sequence