SMTL ID : 7n4u.1

Structure of 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: 2 residues within 4Å: Chain A: N.909, V.1005 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: Q.399, H.400, N.1037 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: 2 residues within 4Å: Chain B: N.909, V.1005 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain B: Q.399, H.400, N.1037 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: N.431, E.566 No protein-ligand interaction detected (PLIP) NAG.8: 2 residues within 4Å: Chain A: Q.455, N.464 No protein-ligand interaction detected (PLIP) 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.506 NAG.16: 2 residues within 4Å: Chain B: N.431, E.566 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain B: Q.455, N.464 No protein-ligand interaction detected (PLIP) 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.506

4 x CLR: CHOLESTEROL(Non-covalent)

CLR.11: 5 residues within 4Å: Chain A: L.370, T.373, L.633, L.677, L.699 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.370, A:L.633, A:L.677, A:L.699 CLR.12: 5 residues within 4Å: Chain A: F.1155, L.1158, W.1159, L.1245, L.1248 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.1155, A:L.1158, A:W.1159, A:W.1159, A:L.1245 CLR.20: 5 residues within 4Å: Chain B: L.370, T.373, L.633, L.677, L.699 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.370, B:L.633, B:L.677, B:L.699 CLR.21: 5 residues within 4Å: Chain B: F.1155, L.1158, W.1159, L.1245, L.1248 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.1155, B:L.1158, B:W.1159, B:W.1159, B:L.1245

2 x VIV: (2R)-2,5,7,8-TETRAMETHYL-2-[(4R,8R)-4,8,12-TRIMETHYLTRIDECYL]CHROMAN-6-OL(Non-covalent)

VIV.13: 16 residues within 4Å: Chain A: L.382, W.383, F.404, T.407, Q.409, L.621, I.625, Q.873, Y.886, L.890, F.894, I.1097, T.1098, F.1101, Y.1102, L.1234 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.382, A:W.383, A:W.383, A:F.404, A:T.407, A:L.621, A:I.625, A:Q.873, A:L.890, A:F.894, A:I.1097, A:T.1098, A:F.1101, A:F.1101, A:L.1234 VIV.22: 16 residues within 4Å: Chain B: L.382, W.383, F.404, T.407, Q.409, L.621, I.625, Q.873, Y.886, L.890, F.894, I.1097, T.1098, F.1101, Y.1102, L.1234 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.382, B:W.383, B:W.383, B:F.404, B:T.407, B:L.621, B:I.625, B:Q.873, B:L.890, B:F.894, B:I.1097, B:T.1098, B:F.1101, B:F.1101, B:L.1234

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

POV.14: 11 residues within 4Å: Chain A: S.350, W.351, P.352, L.353, T.354, V.357, L.358, P.362 Chain B: L.336, L.337, L.785 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.354, A:T.354, A:V.357, A:P.362, B:L.337, B:L.785 Hydrogen bonds: A:L.353, A:T.354, A:T.354 pi-Cation interactions: A:W.351 POV.15: 11 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, P.362 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:T.354, B:T.354, B:V.357, B:P.362, A:L.337, A:L.785 Hydrogen bonds: B:L.353, B:T.354, 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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