SMTL ID : 7dfz.1

Cryo_EM structure of delta N-NPC1L1-EZE

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.1: 2 residues within 4Å: Chain A: W.457, N.464 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.4: 2 residues within 4Å: Chain A: N.909, S.912 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 1 residues within 4Å: Chain A: N.506 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.3: 2 residues within 4Å: Chain A: N.497, L.500 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.5: 3 residues within 4Å: Chain A: Q.399, H.400, N.1037 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: R.421, N.431, K.562 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.562 NAG.7: 1 residues within 4Å: Chain A: N.927 No protein-ligand interaction detected (PLIP) NAG.8: 4 residues within 4Å: Chain A: P.415, N.416, G.609, Q.612 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.612 NAG.9: 1 residues within 4Å: Chain A: N.1075 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.479 No protein-ligand interaction detected (PLIP)

1 x H56: (3~{R},4~{S})-1-(4-fluorophenyl)-3-[(3~{S})-3-(4-fluorophenyl)-3-oxidanyl-propyl]-4-(4-hydroxyphenyl)azetidin-2-one(Non-covalent)

H56.11: 20 residues within 4Å: Chain A: V.380, L.382, W.383, L.621, I.625, V.697, I.698, A.768, F.772, L.871, D.872, Q.873, L.875, A.876, F.1101, Y.1102, V.1166, L.1234, F.1238, F.1239 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.380, A:L.382, A:W.383, A:L.621, A:I.698, A:A.768, A:L.871, A:L.871, A:L.875, A:A.876, A:V.1166, A:L.1234, A:L.1234 Hydrogen bonds: A:L.875

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.12: 6 residues within 4Å: Chain A: W.347, W.351, I.355, L.358, S.359, S.789 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.347, A:L.358 Hydrogen bonds: A:L.785 CLR.13: 3 residues within 4Å: Chain A: F.687, L.690, F.759 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.687, A:L.690, A:F.759 CLR.14: 9 residues within 4Å: Chain A: L.370, V.371, T.373, E.374, L.633, M.681, M.684, L.699, P.703 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.370 Hydrogen bonds: A:L.699 CLR.15: 5 residues within 4Å: Chain A: F.1155, L.1158, W.1159, L.1245, L.1248 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.1158, A:W.1159, A:W.1159, A:L.1245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hu, M. et al., Structural insights into the mechanism of human NPC1L1-mediated cholesterol uptake. Sci Adv (2021)

Release Date

2021-08-11

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.
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NPC1-like intracellular cholesterol transporter 1