MolNFT v1 · #119140 · protein
Cryo-EM structure of gamma secretase in class 2 of the apo- state ensemble
5FN4 · Nicastrin: “Cryo-EM structure of gamma secretase in class 2 of the apo- state ensemble”. Electron microscopy, 17 pockets (best druggability 0.71). MolNFT v1 #119140 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5FN4
- Type
- protein
- Length
- 1,250 residues
- Chains
- 5
- 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
- 17 · best druggability 0.71
Structure
electron microscopy · 5 distinct chains · 54% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nicastrin | protein | 665 | 31% helix, 14% strand | Q92542 |
| B | Presenilin-1 (EC 3.4.23.-) | protein | 217 | 80% helix, 1% strand | P49768 |
| C | Gamma-secretase subunit aph-1A | protein | 243 | 80% helix, 0% strand | Q96BI3 |
| D | Gamma-secretase subunit pen-2 | protein | 100 | 75% helix, 3% strand | Q9NZ42 |
| G | Poly ala chain | protein | 25 | 92% helix, 0% strand | — |
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 580 | 0.71 | 0.78 | 38 | empty |
| 2 | 466 | 0.69 | 0.79 | 36 | empty |
| 3 | 330 | 0.62 | 0.78 | 29 | empty |
| 4 | 255 | 0.59 | 0.79 | 44 | empty |
| 5 | 90 | 0.57 | 0.86 | 25 | empty |
Interfaces
7 interfaces between chains.
- B–C · 1765 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1690 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 1182 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 570 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 511 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 5FN4 · Cryo-EM structure of gamma secretase in class 2 of the apo- state ensemble · 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 0.95
- 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 5FN4 · PDBe 5FN4 · UniProt Q92542 · UniProt P49768 · UniProt Q96BI3 · UniProt Q9NZ42
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