SMTL ID : 8kco.1

Cryo-EM structure of human gamma-secretase in complex with RO4929097

Coordinates

PDB Format Compare

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: 4 residues within 4Å: Chain A: R.38, P.43, N.45, E.188 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:R.38 NAG-NAG.3: 6 residues within 4Å: Chain A: Y.152, V.383, L.431, A.433, R.434, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: W.533, I.537, 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: 7 residues within 4Å: Chain A: S.544, Y.545, L.546, G.547, P.550, L.551, 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: 8 residues within 4Å: Chain A: N.55, T.57, H.58, F.145, H.158, 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, V.390 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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: 3 residues within 4Å: Chain A: G.504, T.505, N.506 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.505 NAG.10: 4 residues within 4Å: Chain A: N.264, T.266, G.267, D.598 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.267 NAG.11: 2 residues within 4Å: Chain A: D.185, N.187 No protein-ligand interaction detected (PLIP) NAG.12: 1 residues within 4Å: Chain A: N.580 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.580

1 x N60: 2,2-dimethyl-N-[(7S)-6-oxo-5,7-dihydrobenzo[d][1]benzazepin-7-yl]-N'-(2,2,3,3,3-pentafluoropropyl)propanediamide(Non-covalent)

N60.13: 15 residues within 4Å: Chain B: V.261, V.272, I.287, V.379, K.380, L.381, G.382, D.385, T.421, L.425, K.429, K.430, A.431, L.432, A.434 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.272, B:I.287, B:K.380, B:T.421 Hydrogen bonds: B:K.380, B:K.380, B:K.380, B:G.382, B:L.432, B:L.432 pi-Cation interactions: B:K.380

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

PC1.14: 9 residues within 4Å: Chain B: A.98, K.101, S.102, D.403, W.404 Chain C: F.6, I.135, A.139, L.142 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:A.98, B:W.404, B:W.404 Hydrogen bonds: B:D.403 Salt bridges: B:K.101 PC1.18: 13 residues within 4Å: Chain A: I.690, A.694, F.698 Chain C: L.20, T.24, S.113, R.115, Q.116, Y.119, F.173, G.225, F.229, A.232 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:L.20, C:Y.119, C:F.173, C:F.229, C:A.232, A:I.690 Hydrogen bonds: C:S.113, C:Q.116

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 6 residues within 4Å: Chain C: Y.69, I.73, L.199, G.202, F.205, L.206 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.69, C:I.73, C:L.199, C:F.205 CLR.16: 4 residues within 4Å: Chain C: R.186, S.223, W.227, I.230 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.227, C:I.230 CLR.17: 5 residues within 4Å: Chain C: Y.155, L.158, F.162, L.214, Y.218 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.155, C:L.158, C:F.162, C:F.162, C:L.214, C:Y.218

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, X. et al., CryoEM structure of PS1-containing gamma-secretase in complex with MRK-560. To Be Published

Release Date

2024-08-14

Peptides

Nicastrin: A
Presenilin-1: 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-1

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

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