Research workbench
Crystal structure of app E2 domain in complex with DR6 crd domain
Analyse Crystal structure of app E2 domain in complex with DR6 crd domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YN0
- Type
- protein
- Length
- 370 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tumor necrosis factor receptor superfamily member 21; Amyloid beta A4 protein
- UniProt
- Q9EPU5, P12023
- Ligands
- NAG, MG
- Pockets
- 5 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tumor necrosis factor receptor superfamily member 21 | protein | 168 | 2% helix, 38% strand | Q9EPU5 |
| B | Amyloid beta A4 protein | protein | 202 | 93% helix, 0% strand | P12023 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.45 | 0.78 | 19 | empty |
| 2 | 83 | 0.43 | 0.80 | 17 | empty |
| 3 | 138 | 0.42 | 0.75 | 25 | empty |
| 4 | 62 | 0.36 | 0.78 | 14 | empty |
| 5 | 64 | 0.34 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 775 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4YN0 · Crystal structure of APP E2 domain in complex with DR6 CRD domain · the same entry in another collection · chain A against A, TM-score 1.00
- P12023 · AlphaFold monomer V2.0 prediction for amyloid-beta A4 protein (P12023) · a predicted model of the same protein · chain B against A, TM-score 0.88
- Q9EPU5 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain A against A, TM-score 0.84
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 Q9EPU5
- Every structure of UniProt P12023
- Elsewhere: RCSB PDB 4YN0 · PDBe 4YN0 · UniProt Q9EPU5 · UniProt P12023
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