MolNFT v1 · #152302 · protein
Cryo-EM structure of gamma secretase in complex with a notch fragment
6IDF: “Cryo-EM structure of gamma secretase in complex with a notch fragment”. Electron microscopy, 4 ligands (PC1, CLR, NAG). MolNFT v1 #152302 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IDF
- Type
- protein
- Length
- 1,363 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- Q92542, P49768, Q96BI3, Q9NZ42
- Ligands
- PC1, CLR, NAG, BMA
Structure
electron microscopy · 5 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 667 | — | Q92542 |
| B | — | protein | 312 | — | P49768 |
| C | — | protein | 243 | — | Q96BI3 |
| D | — | protein | 100 | — | Q9NZ42 |
| E | — | protein | 41 | — | — |
Ligands and binding sites
- PC1 · 1,2-diacyl-sn-glycero-3-phosphocholine · ligand · 4 copies · chains B, C, A, D
- CLR · Cholesterol · ligand · 3 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, C
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 6IDF · Cryo-EM structure of gamma secretase in complex with a Notch fragment · the same entry in another collection · chain E against E, 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 0.97
- P49768 · AlphaFold monomer V2.0 prediction for presenilin-1 (P49768) · a predicted model of the same protein · chain B 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
- 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
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 6IDF · PDBe 6IDF · UniProt Q92542 · UniProt P49768 · UniProt Q96BI3 · UniProt Q9NZ42
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