Research workbench
Cryo-EM structure of gamma secretase in complex with a drug dapt
Analyse Cryo-EM structure of gamma secretase in complex with a drug dapt in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FN2
- Type
- protein
- Length
- 1,309 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
- Pockets
- 14 · best druggability 0.81
Structure
electron microscopy · 4 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicastrin | protein | 665 | 31% helix, 15% strand | Q92542 |
| B | Presenilin-1 (EC 3.4.23.-) | protein | 301 | 75% helix, 1% strand | P49768 |
| C | Gamma-secretase subunit aph-1A | protein | 243 | 81% helix, 0% strand | Q96BI3 |
| D | Gamma-secretase subunit pen-2 | protein | 100 | 69% helix, 3% strand | Q9NZ42 |
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.81 | 0.84 | 77 | empty |
| 2 | 574 | 0.70 | 0.78 | 37 | empty |
| 3 | 433 | 0.66 | 0.78 | 44 | empty |
| 4 | 283 | 0.59 | 0.77 | 26 | empty |
| 5 | 336 | 0.53 | 0.74 | 47 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1749 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1689 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1247 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 576 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 569 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5FN2 · Cryo-EM structure of gamma secretase in complex with a drug DAPT · the same entry in another collection · chain D against D, TM-score 1.00
- Q92542 · AlphaFold monomer V2.0 prediction for nicastrin (Q92542) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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
- 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 0.96
- P49768 · AlphaFold monomer V2.0 prediction for presenilin-1 (P49768) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 5FN2 · PDBe 5FN2 · UniProt Q92542 · UniProt P49768 · UniProt Q96BI3 · UniProt Q9NZ42
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