SMTL ID : 6iyc.1

Recognition of the Amyloid Precursor Protein by Human gamma-secretase

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-1-mer

Ligands

5 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: R.38, I.42, P.43, L.44, N.45, E.188 Chain C: H.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.150 NAG-NAG.3: 6 residues within 4Å: Chain A: Y.152, V.383, K.386, L.431, A.433, N.435 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.383 NAG-NAG.4: 5 residues within 4Å: Chain A: W.533, S.536, N.573, P.608, R.619 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.530, Q.535, L.546 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: S.544, Y.545, G.547, P.550, L.551, N.562 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.544, A:S.544

1 x NAG- NAG- BMA- BMA- BMA: beta-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.2: 6 residues within 4Å: Chain A: N.55, H.58, F.145, Y.173, E.174, W.648 No protein-ligand interaction detected (PLIP)

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

NAG.7: 2 residues within 4Å: Chain A: N.387, S.389 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.387, A:S.389 NAG.8: 2 residues within 4Å: Chain A: N.464, D.482 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.482 Hydrogen bonds: A:D.482 NAG.9: 2 residues within 4Å: Chain A: T.505, N.506 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.505, A:T.505 NAG.10: 4 residues within 4Å: Chain A: N.264, T.266, G.267, D.598 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.267, A:D.598 NAG.11: 1 residues within 4Å: Chain A: N.187 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.580 No protein-ligand interaction detected (PLIP)

2 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.13: 8 residues within 4Å: Chain B: A.98, K.101, D.403, W.404 Chain C: F.6, I.135, A.139, L.142 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:A.98, B:K.101, B:W.404, C:I.135 PC1.17: 14 residues within 4Å: Chain A: S.683, I.690, A.694, D.695, F.698, A.700 Chain C: L.20, T.24, S.113, Q.116, Y.119, F.173, G.225, F.229 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.20, C:T.24, C:Y.119, C:F.173, C:F.229 Hydrogen bonds: C:S.113, C:Q.116, A:D.695

3 x CLR: CHOLESTEROL(Non-covalent)(Covalent)

CLR.14: 5 residues within 4Å: Chain C: R.66, Y.69, G.202, F.205, L.206 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.69, C:F.205, C:F.205, C:L.206 CLR.15: 4 residues within 4Å: Chain C: W.188, L.192, S.223, W.227 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.188, C:W.227, C:W.227, C:W.227, C:W.227 CLR.16: 5 residues within 4Å: Chain C: Y.155, F.162, Y.210, L.214, L.215 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.155, C:F.162, C:Y.210, C:L.214, C:L.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, R. et al., Recognition of the amyloid precursor protein by human gamma-secretase. Science (2019)

Release Date

2019-01-23

Peptides

Nicastrin: A
Presenilin-1: B
Gamma-secretase subunit APH-1A: C
Gamma-secretase subunit PEN-2: D
Amyloid-beta A4 protein: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

Membrane

We predict this structure to be a membrane protein.
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Nicastrin

Presenilin-1

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

Amyloid-beta A4 protein

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