SMTL ID : 8kct.1

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

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: P.43, N.45, E.188 Chain B: H.150 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.150 NAG-NAG.3: 3 residues within 4Å: Chain A: V.383, A.433, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: W.533, N.573, G.576, T.577, R.619, V.621 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.530, Q.535, L.546, D.548 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: S.544, Y.545, G.547, 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: 6 residues within 4Å: Chain A: N.55, T.57, H.58, F.145, Y.173, 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:N.387 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: G.504, 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.267, A:N.596 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 No protein-ligand interaction detected (PLIP)

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

CLR.13: 3 residues within 4Å: Chain B: Y.69, G.202, L.206 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.69, B:L.206 CLR.14: 3 residues within 4Å: Chain B: R.186, L.192, W.227 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.192, B:W.227, B:W.227, B:W.227 CLR.15: 6 residues within 4Å: Chain B: Y.155, T.159, F.162, E.211, L.214, Y.218 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Y.155, B:F.162, B:E.211, B:L.214, B:Y.218

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

PC1.16: 17 residues within 4Å: Chain A: S.683, T.687, I.690, A.694, F.698 Chain B: L.20, T.24, S.113, R.115, Q.116, Y.119, F.173, V.176, G.225, A.228, F.229, A.232 9 PLIP interactions: 2 interactions with chain A, 7 interactions with chain B Hydrophobic interactions: A:I.690, A:F.698, B:T.24, B:Y.119, B:F.173, B:F.229, B:F.229, B:A.232 Hydrogen bonds: B:Q.116 PC1.17: 9 residues within 4Å: Chain B: F.6, I.135, A.139, L.142 Chain D: A.98, K.101, S.102, D.403, W.404 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:W.404, B:I.135 Hydrogen bonds: D:D.403 Salt bridges: D:K.101

1 x O6U: (2S)-2-[[(2S)-6,8-bis(fluoranyl)-1,2,3,4-tetrahydronaphthalen-2-yl]amino]-N-[1-[1-(2,2-dimethylpropylamino)-2-methyl-propan-2-yl]imidazol-4-yl]pentanamide(Non-covalent)

O6U.18: 14 residues within 4Å: Chain D: Y.77, V.261, L.268, L.271, V.272, L.282, I.287, V.379, K.380, L.381, L.425, K.430, A.431, L.432 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:V.261, D:L.268, D:V.272, D:L.282, D:I.287, D:L.381, D:A.431 Hydrogen bonds: D:K.380, D:K.380, D:L.432, D:L.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guo, X. et al., Structural Basis of gamma-secretase inhibition by anti-cancer clinical drugs. To Be Published

Release Date

2024-08-14

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

C
D

D
B

Membrane

We predict this structure to be a membrane protein.
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Nicastrin

Gamma-secretase subunit APH-1A

Gamma-secretase subunit PEN-2

Presenilin-1

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