MolNFT v1 · #111307 · protein
Crystal structure of app E2 domain in complex with DR6 crd domain
4YN0 · Tumor necrosis factor receptor superfamily member 21: “Crystal structure of app E2 domain in complex with DR6 crd domain”. X-ray diffraction, 2 ligands (NAG, MG), 5 pockets (best druggability 0.45). MolNFT v1 #111307 on GenesisL1…
- 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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