SMTL ID : 8kcs.1

Cryo-EM structure of human gamma-secretase in complex with BMS906024

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, P.43, N.45, E.188 Chain C: H.150 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.150 NAG-NAG.3: 6 residues within 4Å: Chain A: Y.152, V.383, K.386, N.387, A.433, N.435 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain A: W.533, S.536, N.573, G.576, T.577, V.578, 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: 6 residues within 4Å: Chain A: S.544, Y.545, 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)(Non-covalent)

NAG.7: 1 residues within 4Å: Chain A: N.387 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.482 NAG.9: 2 residues within 4Å: Chain A: T.505, N.506 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.505, A:N.506 NAG.10: 5 residues within 4Å: Chain A: N.264, T.266, N.596, D.598, L.599 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.266, A:T.266, A:N.596 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 No protein-ligand interaction detected (PLIP)

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

PC1.13: 7 residues within 4Å: Chain B: A.98, K.101, S.102, D.403, W.404 Chain C: F.6, A.139 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:K.101, B:W.404, B:W.404 Salt bridges: B:K.101 PC1.18: 15 residues within 4Å: Chain A: S.683, A.694 Chain C: P.16, L.20, T.24, S.113, R.115, Q.116, Y.119, F.173, V.176, G.225, A.228, F.229, A.232 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:P.16, C:L.20, C:T.24, C:Y.119, C:F.173, C:F.229, C:A.232 Hydrogen bonds: C:Q.116

1 x Q70: (2S,3R)-N'-[(3S)-1-methyl-2-oxidanylidene-5-phenyl-3H-1,4-benzodiazepin-3-yl]-2,3-bis[3,3,3-tris(fluoranyl)propyl]butanediamide(Non-covalent)

Q70.14: 19 residues within 4Å: Chain B: L.85, V.272, Q.276, G.378, V.379, K.380, L.381, G.382, D.385, L.418, T.421, L.422, L.425, K.429, K.430, A.431, L.432, P.433, A.434 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.272, B:L.381 Hydrogen bonds: B:K.380, B:K.380, B:G.382, B:D.385, B:L.432, B:A.434

3 x CLR: CHOLESTEROL(Non-covalent)

CLR.15: 6 residues within 4Å: Chain C: Y.69, L.198, L.199, G.202, F.205, L.206 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.69, C:F.205 CLR.16: 4 residues within 4Å: Chain C: R.186, L.192, W.227, I.230 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.192, C:W.227, C:W.227, C:I.230 CLR.17: 5 residues within 4Å: Chain C: Y.155, T.159, F.162, L.214, Y.218 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:Y.155, C:T.159, C:F.162, C:F.162, C:L.214, C:Y.218, C:Y.218

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
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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