SMTL ID : 7d8x.1

CryoEM structure of human gamma-secretase in complex with E2012 and L685458

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: 6 residues within 4Å: Chain A: R.38, I.42, P.43, L.44, N.45, E.188 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:R.38 Hydrogen bonds: A:R.38 NAG-NAG.3: 5 residues within 4Å: Chain A: Y.152, V.383, N.387, A.433, N.435 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.383 NAG-NAG.4: 7 residues within 4Å: Chain A: W.533, N.573, G.576, T.577, V.578, 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: 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: 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)

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: 2 residues within 4Å: Chain A: N.464, D.482 1 PLIP interactions: 1 interactions with chain A 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: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 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: 6 residues within 4Å: Chain B: K.101, S.102, W.404 Chain C: I.135, A.139, L.142 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:I.135, B:K.101, B:W.404 Salt bridges: B:K.101 PC1.20: 17 residues within 4Å: Chain A: S.683, T.687, I.690, N.691, 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: 2 interactions with chain A, 8 interactions with chain C Hydrophobic interactions: A:I.690, A:F.698, C:L.20, C:T.24, C:Y.119, C:F.173, C:F.229, C:A.232 Hydrogen bonds: C:Q.116 Salt bridges: C:R.115

1 x GZR: 1-[(1S)-1-(4-fluorophenyl)ethyl]-3-[[3-methoxy-4-(4-methylimidazol-1-yl)phenyl]methylidene]piperidin-2-one(Non-covalent)

GZR.14: 8 residues within 4Å: Chain A: I.242, N.243 Chain B: F.105, Y.106, F.177, I.180, V.236, Y.240 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.177, B:F.177, B:V.236 Hydrogen bonds: B:Y.106, B:Y.240 pi-Stacking: B:Y.240

1 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.15: 8 residues within 4Å: Chain B: R.128, W.244, W.247, A.251, T.440, L.443, F.447, Y.451 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.244, B:A.251, B:L.443, B:F.447, B:F.447, B:F.447 Salt bridges: B:R.128

1 x FTO: ~{tert}-butyl ~{N}-[(2~{S},3~{R},5~{R})-6-[[(2~{S})-1-[[(2~{S})-1-azanyl-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]amino]-3-oxidanyl-6-oxidanylidene-1-phenyl-5-(phenylmethyl)hexan-2-yl]carbamate(Non-covalent)

FTO.16: 21 residues within 4Å: Chain B: Y.77, L.85, D.257, L.268, L.271, V.272, L.286, I.287, V.379, K.380, L.381, G.382, L.383, G.384, D.385, T.421, L.425, A.431, L.432, A.434, L.435 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.85, B:L.268, B:L.268, B:L.271, B:V.272, B:V.379, B:K.380, B:K.380, B:L.381, B:T.421, B:A.431, B:L.435 Hydrogen bonds: B:Y.77, B:Y.77, B:D.257, B:K.380, B:K.380, B:G.382, B:G.384, B:L.432, B:L.432, B:A.434

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.17: 5 residues within 4Å: Chain C: I.73, L.199, G.202, F.205, L.206 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.73, C:F.205 CLR.18: 4 residues within 4Å: Chain C: W.188, L.192, S.223, W.227 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:W.188, C:L.192, C:W.227, C:W.227, C:W.227, C:W.227 Hydrogen bonds: C:S.223 CLR.19: 6 residues within 4Å: Chain C: T.159, F.162, Y.210, E.211, L.214, L.215 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.162, C:Y.210, C:E.211, C:L.214, C:L.215

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, G. et al., Structural basis of gamma-secretase inhibition and modulation by small molecule drugs. Cell (2021)

Release Date

2021-01-27

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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