SMTL ID : 6w5v.1

NPC1-NPC2 complex structure at pH 5.5

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-mer

Ligands

4 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.478, T.536 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: L.929, N.931 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: G.65, F.66, N.106, N.222 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 6 residues within 4Å: Chain B: E.36, N.38, N.58, T.60, S.108, L.110 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.2: 7 residues within 4Å: Chain A: I.419, A.427, D.428, P.430, D.551, N.554, N.557 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.428, A:D.428, A:D.428

10 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.6: 1 residues within 4Å: Chain A: N.452 No protein-ligand interaction detected (PLIP) 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: 2 residues within 4Å: Chain A: N.524, H.530 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.530 NAG.9: 3 residues within 4Å: Chain A: Q.442, 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: 1 residues within 4Å: Chain A: N.961 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain A: Y.475, N.968, S.970, N.1006 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:N.1006 Hydrogen bonds: A:N.968 NAG.13: 1 residues within 4Å: Chain A: N.1064 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain A: N.158, R.161 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.158, A:R.161 NAG.17: 1 residues within 4Å: Chain B: N.135 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.135

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 12 residues within 4Å: Chain A: W.27, N.41, N.86, L.87, P.90, F.108, T.112, L.176, M.193, N.198, Q.200, F.203 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:N.86, A:L.87, A:F.108, A:F.108, A:N.198, A:Q.200, A:F.203 Hydrogen bonds: A:N.41 CLR.16: 10 residues within 4Å: Chain A: P.377, W.381, I.609, L.613, I.685, A.756, Q.862, S.865, F.1087, Y.1225 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:P.377, A:W.381, A:W.381, A:W.381, A:I.609, A:L.613, A:I.685, A:F.1087, A:Y.1225 CLR.18: 8 residues within 4Å: Chain B: L.49, V.57, V.83, F.85, Y.119, P.120, L.124, V.126 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.49, B:V.57, B:V.83, B:F.85, B:F.85, B:F.85, B:Y.119, B:L.124, B:V.126

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
NPC intracellular cholesterol transporter 2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Membrane

We predict this structure to be a membrane protein.
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NPC intracellular cholesterol transporter 1

NPC intracellular cholesterol transporter 2

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