SMTL ID : 6lr4.1

Molecular basis for inhibition of human gamma-secretase by small molecule

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: 5 residues within 4Å: Chain A: R.38, I.42, P.43, N.45, E.188 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: V.383, L.431, A.433, R.434, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: W.533, I.537, N.573, G.576, T.577, P.608, R.619, V.621 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: 5 residues within 4Å: Chain A: S.544, Y.545, 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, H.158, Y.173, E.174 No protein-ligand interaction detected (PLIP)

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

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 Hydrogen bonds: A:N.464, A:D.482 NAG.9: 1 residues within 4Å: Chain A: N.506 No protein-ligand interaction detected (PLIP) 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 No protein-ligand interaction detected (PLIP)

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

PC1.13: 9 residues within 4Å: Chain B: V.94, K.101, S.102, W.404 Chain C: F.6, I.135, L.138, A.139, L.142 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:V.94, B:W.404, C:I.135 Hydrogen bonds: B:D.403 Salt bridges: B:K.101 PC1.18: 12 residues within 4Å: Chain A: N.691, A.694, F.698 Chain C: L.20, T.24, S.113, R.115, Q.116, Y.119, F.173, 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:F.698 Hydrogen bonds: C:S.113, C:Q.116

1 x ESF: (2S)-2-hydroxy-3-methyl-N-[(2S)-1-[[(5S)-3-methyl-4-oxo-2,5-dihydro-1H-3-benzazepin-5-yl]amino]-1-oxopropan-2-yl]butanamide(Non-covalent)

ESF.14: 10 residues within 4Å: Chain B: L.282, V.379, K.380, G.382, D.385, L.425, K.430, A.431, L.432, A.434 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:L.282, B:A.431 Hydrogen bonds: B:K.380, B:K.380, B:D.385, B:L.432, B:L.432, B:A.434

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 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Y.69, C:I.73, C:F.205, C:F.205, C:L.206 CLR.16: 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:L.192, C:W.227, C:W.227, C:W.227 CLR.17: 5 residues within 4Å: Chain C: Y.155, Y.210, E.211, L.214, L.215 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:Y.155, C:Y.210, C:E.211, 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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