SMTL ID : 6w5r.1

NPC1 structure in Nanodisc

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: 7 residues within 4Å: Chain A: G.65, F.66, F.68, N.106, E.110, R.116, N.222 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.68 NAG-NAG.2: 3 residues within 4Å: Chain A: N.476, N.478, T.536 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.3: 8 residues within 4Å: Chain A: K.417, A.427, D.428, P.430, D.551, N.554, N.556, N.557 No protein-ligand interaction detected (PLIP)

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.4: 1 residues within 4Å: Chain A: 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.158 No protein-ligand interaction detected (PLIP) NAG.6: 1 residues within 4Å: Chain A: N.452 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.452 NAG.7: 1 residues within 4Å: Chain A: N.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.459 NAG.8: 4 residues within 4Å: Chain A: N.524, T.526, H.530, P.1009 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.1009 NAG.9: 4 residues within 4Å: Chain A: Q.442, N.596, P.597, N.598 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.442 NAG.10: 1 residues within 4Å: Chain A: N.916 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.916 NAG.11: 3 residues within 4Å: Chain A: N.961, A.975, V.977 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.977 Hydrogen bonds: A:N.961 NAG.12: 4 residues within 4Å: Chain A: Y.475, N.968, N.1006, N.1008 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.1006 Hydrogen bonds: A:N.968, A:N.1008 NAG.13: 2 residues within 4Å: Chain A: I.1061, N.1064 No protein-ligand interaction detected (PLIP)

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.14: 14 residues within 4Å: Chain A: N.41, Q.79, T.82, L.83, N.86, L.87, F.108, T.112, L.176, M.193, N.198, Q.200, A.201, P.202 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Q.79, A:L.83, A:L.83, A:F.108, A:L.176, A:Q.200, A:P.202 Hydrogen bonds: A:N.41, A:Q.79

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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