SMTL ID : 7n4v.1

Structure of cholesterol-bound human NPC1L1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-dimer

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: 2 residues within 4Å: Chain A: N.497, T.499 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: N.909, S.912, V.1005, Q.1043 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Q.399, H.400, N.1037, L.1045 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.497, T.499 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain B: N.909, S.912, V.1005, Q.1043 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: Q.399, H.400, N.1037, L.1045 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: S.419, N.431 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.431 Hydrogen bonds: A:S.419, A:S.419 NAG.8: 1 residues within 4Å: Chain A: N.464 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.464 NAG.9: 1 residues within 4Å: Chain A: N.1075 No protein-ligand interaction detected (PLIP) NAG.10: 2 residues within 4Å: Chain A: N.506, Q.515 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.506, A:Q.515 NAG.16: 2 residues within 4Å: Chain B: S.419, N.431 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.431 Hydrogen bonds: B:S.419, B:S.419 NAG.17: 1 residues within 4Å: Chain B: N.464 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.464 NAG.18: 1 residues within 4Å: Chain B: N.1075 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain B: N.506, Q.515 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.506, B:Q.515

6 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 15 residues within 4Å: Chain A: P.379, L.382, W.383, L.621, V.697, I.698, V.701, A.768, V.769, F.772, Q.873, A.876, F.1101, L.1234, F.1239 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.382, A:W.383, A:W.383, A:W.383, A:L.621, A:V.697, A:V.701, A:A.768, A:V.769, A:F.772, A:F.772, A:F.772, A:Q.873, A:A.876, A:L.1234 Hydrogen bonds: A:Q.873 CLR.12: 7 residues within 4Å: Chain A: L.370, T.373, L.375, L.633, Y.640, L.677, L.699 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.370, A:L.375, A:L.633, A:L.677, A:L.699 CLR.13: 5 residues within 4Å: Chain A: F.1155, L.1158, W.1159, L.1245, L.1248 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.1155, A:F.1155, A:L.1158, A:W.1159, A:W.1159, A:W.1159, A:L.1245 CLR.20: 16 residues within 4Å: Chain B: P.379, L.382, W.383, L.621, V.697, I.698, V.701, A.768, V.769, F.772, Q.873, A.876, F.1101, V.1166, L.1234, F.1239 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:L.382, B:W.383, B:W.383, B:W.383, B:L.621, B:V.697, B:I.698, B:V.701, B:A.768, B:V.769, B:F.772, B:F.772, B:Q.873, B:A.876, B:V.1166, B:L.1234 Hydrogen bonds: B:Q.873 CLR.21: 7 residues within 4Å: Chain B: L.370, T.373, L.375, L.633, Y.640, L.677, L.699 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.370, B:L.375, B:L.633, B:L.677, B:L.699 CLR.22: 5 residues within 4Å: Chain B: F.1155, L.1158, W.1159, L.1245, L.1248 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.1155, B:F.1155, B:L.1158, B:W.1159, B:W.1159, B:W.1159, B:L.1245

2 x POV: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate(Non-covalent)

POV.14: 12 residues within 4Å: Chain A: S.350, W.351, P.352, L.353, T.354, V.357, L.358, I.361, P.362 Chain B: L.336, L.337, L.785 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:V.357, A:I.361, A:P.362, B:L.337, B:L.785 Hydrogen bonds: A:L.353, A:T.354 pi-Cation interactions: A:W.351 POV.15: 12 residues within 4Å: Chain A: L.336, L.337, L.785 Chain B: S.350, W.351, P.352, L.353, T.354, V.357, L.358, I.361, P.362 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.357, B:I.361, B:P.362, A:L.337, A:L.785 Hydrogen bonds: B:L.353, B:T.354 pi-Cation interactions: B:W.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Long, T. et al., Structures of dimeric human NPC1L1 provide insight into mechanisms for cholesterol absorption. Sci Adv (2021)

Release Date

2021-09-01

Peptides

Isoform 2 of NPC1-like intracellular cholesterol transporter 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Membrane

We predict this structure to be a membrane protein.
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Isoform 2 of NPC1-like intracellular cholesterol transporter 1

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