SMTL ID : 5kwy.1

Structure of human NPC1 middle lumenal domain bound to NPC2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

hetero-2-2-mer

Ligands

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

NAG.1: 4 residues within 4Å: Chain C: N.39, T.41, S.89, L.91 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.91 Hydrogen bonds: C:N.39, C:T.41 NAG.2: 2 residues within 4Å: Chain C: Q.112, N.116 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.112 NAG.4: 4 residues within 4Å: Chain D: N.39, T.41, S.89, L.91 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.91 Hydrogen bonds: D:N.39, D:T.41, D:S.89 NAG.5: 3 residues within 4Å: Chain D: Q.110, Q.112, N.116 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.112, D:N.116 Water bridges: D:Q.110, D:S.118

2 x C3S: CHOLEST-5-EN-3-YL HYDROGEN SULFATE(Non-covalent)

C3S.3: 11 residues within 4Å: Chain C: V.20, L.30, Y.36, G.57, F.66, L.94, V.96, Y.100, P.101, I.124, I.128 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.20, C:Y.36, C:F.66, C:F.66, C:L.94, C:V.96, C:Y.100, C:Y.100, C:I.124, C:I.128 C3S.6: 14 residues within 4Å: Chain D: V.20, L.30, Y.36, V.38, G.57, F.66, L.94, V.96, Y.100, P.101, I.103, L.105, W.109, I.128 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:V.20, D:V.20, D:Y.36, D:V.38, D:F.66, D:F.66, D:F.66, D:F.66, D:F.66, D:L.94, D:V.96, D:Y.100, D:Y.100, D:Y.100, D:I.103, D:W.109, D:I.128

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, X. et al., Clues to the mechanism of cholesterol transfer from the structure of NPC1 middle lumenal domain bound to NPC2. Proc.Natl.Acad.Sci.USA (2016)

Release Date

2016-08-24

Peptides

Niemann-Pick C1 protein: AB
Epididymal secretory protein E1: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Niemann-Pick C1 protein

Epididymal secretory protein E1