SMTL ID : 7y5x.1

CryoEM structure of PS2-containing gamma-secretase treated with MRK-560

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-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: 5 residues within 4Å: Chain A: R.38, I.42, P.43, N.45, E.188 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:R.38 Hydrogen bonds: A:R.38, A:R.38 NAG-NAG.3: 4 residues within 4Å: Chain A: Y.152, V.383, A.433, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: W.533, S.536, N.573, G.576, V.578, R.619 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.619, A:R.619 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, L.546, G.547, P.550, N.562 No protein-ligand interaction detected (PLIP)

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: 7 residues within 4Å: Chain A: N.55, T.57, 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)(Non-covalent)

NAG.7: 3 residues within 4Å: Chain A: N.387, S.389, V.390 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.387, A:S.389 NAG.8: 1 residues within 4Å: Chain A: N.464 No protein-ligand interaction detected (PLIP) NAG.9: 3 residues within 4Å: Chain A: G.504, T.505, N.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.506 NAG.10: 3 residues within 4Å: Chain A: N.264, T.266, G.267 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.266 NAG.11: 2 residues within 4Å: Chain A: D.185, N.187 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.187 NAG.12: 1 residues within 4Å: Chain A: N.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.580

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

PC1.13: 15 residues within 4Å: Chain A: S.683, I.690, A.694, F.698 Chain C: L.20, T.24, S.113, R.115, Q.116, Y.119, F.173, G.225, A.228, F.229, A.232 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:L.20, C:Y.119, C:Y.119, C:F.173, C:F.229, C:A.232, A:I.690, A:F.698 Hydrogen bonds: C:S.113, C:Q.116 PC1.14: 12 residues within 4Å: Chain B: I.100, V.103, A.104, K.107, S.108, R.110, W.385, L.389 Chain C: F.6, I.135, A.139, L.142 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.100, B:V.103, B:A.104, B:W.385, B:L.389, B:L.389 Hydrogen bonds: B:R.110 Salt bridges: B:K.107

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 5 residues within 4Å: Chain C: Y.69, I.73, G.202, F.205, L.206 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.69, C:I.73, C:F.205, C:F.205 CLR.16: 5 residues within 4Å: Chain C: W.188, S.196, S.223, W.227, I.230 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:W.188, C:W.188, C:W.227, C:W.227, C:I.230 CLR.17: 5 residues within 4Å: Chain C: Y.155, T.159, Y.210, E.211, L.214 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.155, C:Y.155, C:Y.210, C:Y.210, C:E.211

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, X. et al., Molecular basis for isoform-selective inhibition of presenilin-1 by MRK-560. Nat Commun (2022)

Release Date

2022-11-02

Peptides

Nicastrin: A
Presenilin-2: B
Gamma-secretase subunit APH-1A: C
Gamma-secretase subunit PEN-2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Nicastrin

Presenilin-2

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

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