SMTL ID : 6w5s.1

NPC1 structure in GDN micelles at pH 8.0

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

2 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: 4 residues within 4Å: Chain A: N.476, N.478, Q.489, T.536 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: G.65, F.66, F.68, E.110, N.222 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-MAN.2: 8 residues within 4Å: Chain A: I.419, A.427, D.428, P.430, D.551, N.554, N.556, N.557 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.428, A:D.428, A:D.428

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

NAG-NAG-MAN.3: 2 residues within 4Å: Chain A: L.929, N.931 No protein-ligand interaction detected (PLIP)

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

NAG.5: 1 residues within 4Å: Chain A: N.452 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.459 NAG.7: 4 residues within 4Å: Chain A: Q.92, N.524, T.526, H.530 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.92, A:N.524, A:T.526 NAG.8: 4 residues within 4Å: Chain A: Q.442, N.596, P.597, N.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.442, A:N.596 NAG.9: 1 residues within 4Å: Chain A: N.916 No protein-ligand interaction detected (PLIP) NAG.10: 1 residues within 4Å: Chain A: N.961 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.961 NAG.11: 3 residues within 4Å: Chain A: Y.475, N.968, N.1006 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.1006 Hydrogen bonds: A:N.968 NAG.12: 3 residues within 4Å: Chain A: L.1060, I.1061, N.1064 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1064 NAG.13: 3 residues within 4Å: Chain A: N.154, N.158, R.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.161

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 12 residues within 4Å: Chain A: N.41, L.83, N.86, L.87, L.89, P.90, F.108, T.112, M.193, N.198, Q.200, A.201 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.83, A:N.86, A:L.87, A:L.89, A:T.112, A:A.201 Hydrogen bonds: A:N.41

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

POV.15: 10 residues within 4Å: Chain A: L.853, N.854, K.855, V.856, I.858, I.1095, I.1099, G.1103, V.1136, F.1139 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.853, A:N.854, A:V.856, A:I.1099, A:V.1136, A:F.1139, A:F.1139

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Qian, H. et al., Structural Basis of Low-pH-Dependent Lysosomal Cholesterol Egress by NPC1 and NPC2. Cell (2020)

Release Date

2020-06-17

Peptides

NPC 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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NPC intracellular cholesterol transporter 1

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