SMTL ID : 3jd8.1

cryo-EM structure of the full-length human NPC1 at 4.4 angstrom

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

monomer

Ligands

3 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, C.109, E.110, N.222 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: Q.88, N.524, K.1013 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.88 NAG-NAG.4: 3 residues within 4Å: Chain A: Q.442, N.596, N.598 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA.3: 6 residues within 4Å: Chain A: K.417, D.428, P.430, D.551, N.554, N.557 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.428

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.5: 3 residues within 4Å: Chain A: Y.475, N.476, N.478 No protein-ligand interaction detected (PLIP)

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

NAG.6: 3 residues within 4Å: Chain A: N.158, S.244, I.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.158, A:R.161, A:S.244 NAG.7: 2 residues within 4Å: Chain A: Y.571, N.572 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.571, A:N.572 NAG.8: 1 residues within 4Å: Chain A: N.122 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain A: N.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.70 NAG.10: 1 residues within 4Å: Ligands: NAG.11 No protein-ligand interaction detected (PLIP) NAG.11: 5 residues within 4Å: Chain A: A.183, N.185, T.187, N.188 Ligands: NAG.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.183 Hydrogen bonds: A:T.187, A:N.188 NAG.12: 1 residues within 4Å: Chain A: N.1064 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1064 NAG.13: 1 residues within 4Å: Chain A: N.1072 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.1072 NAG.14: 1 residues within 4Å: Chain A: N.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.135 NAG.15: 1 residues within 4Å: Chain A: N.452 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.452 NAG.16: 1 residues within 4Å: Chain A: N.459 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.459

1 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 18 residues within 4Å: Chain A: N.41, Q.79, T.82, L.83, N.86, P.90, F.108, L.111, T.112, L.176, Y.192, M.193, N.198, Q.200, A.201, P.202, F.203, I.205 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:L.83, A:L.83, A:N.86, A:P.90, A:F.108, A:F.108, A:L.111, A:L.176, A:M.193, A:Q.200, A:A.201, A:P.202, A:I.205 Hydrogen bonds: A:N.41, A:Q.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gong, X. et al., The structure of Niemann-Pick C1 protein. To Be Published

Release Date

2016-06-01

Peptides

Niemann-Pick C1 protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Niemann-Pick C1 protein

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