MolNFT v1 · #156036 · protein
Molecular basis for inhibition of human gamma-secretase by small molecule
6LR4 · Nicastrin: “Molecular basis for inhibition of human gamma-secretase by small molecule”. Electron microscopy, 5 ligands (CLR, PC1, ESF), 15 pockets (best druggability 0.82). MolNFT v1 #156036 on GenesisL1: 3D structure, binding sites…
- PDB
- 6LR4
- Type
- protein
- Length
- 1,314 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nicastrin; Presenilin-1; Gamma-secretase subunit aph-1A; Gamma-secretase subunit pen-2
- EC
- 3.4.23.-
- UniProt
- Q92542, P49768, Q96BI3, Q9NZ42
- Ligands
- CLR, PC1, ESF, NAG, BMA
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicastrin | protein | 667 | 30% helix, 17% strand | Q92542 |
| B | Presenilin-1 (EC 3.4.23.-) | protein | 308 | 72% helix, 1% strand | P49768 |
| C | Gamma-secretase subunit aph-1A | protein | 243 | 76% helix, 0% strand | Q96BI3 |
| D | Gamma-secretase subunit pen-2 | protein | 96 | 66% helix, 3% strand | Q9NZ42 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 3 copies · chains C
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 2 copies · chains B, C, A
- 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 · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.82 | 0.82 | 68 | ESF |
| 2 | 80 | 0.75 | 0.98 | 22 | empty |
| 3 | 100 | 0.73 | 0.95 | 31 | empty |
| 4 | 597 | 0.71 | 0.79 | 45 | PC1 |
| 5 | 567 | 0.67 | 0.76 | 34 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1769 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1751 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 1136 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 516 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 475 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 6LR4 · Molecular basis for inhibition of human gamma-secretase by small molecule · the same entry in another collection · chain D against D, TM-score 1.00
- P49768 · AlphaFold monomer V2.0 prediction for presenilin-1 (P49768) · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q92542 · AlphaFold monomer V2.0 prediction for nicastrin (Q92542) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q9NZ42 · AlphaFold monomer V2.0 prediction for gamma-secretase subunit pen-2 (Q9NZ42) · a predicted model of the same protein · chain D against A, TM-score 0.97
- Q96BI3 · AlphaFold monomer V2.0 prediction for gamma-secretase subunit aph-1A (Q96BI3) · a predicted model of the same protein · chain C against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q92542
- Every structure of UniProt P49768
- Every structure of UniProt Q96BI3
- Every structure of UniProt Q9NZ42
- Elsewhere: RCSB PDB 6LR4 · PDBe 6LR4 · UniProt Q92542 · UniProt P49768 · UniProt Q96BI3 · UniProt Q9NZ42
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