Research workbench
X-ray structure of the E2 domain of the human amyloid precursor protein (app) in complex with copper
Analyse X-ray structure of the E2 domain of the human amyloid precursor protein (app)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3UMK
- Type
- protein
- Length
- 184 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amyloid beta A4 protein
- UniProt
- P05067
- Ligands
- CD, CU
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 91% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Amyloid beta A4 protein | protein | 184 | 91% helix, 0% strand | P05067 |
Ligands and binding sites
- CD · Cadmium ion · metal · 7 copies · chains A
- CU · Copper (II) ion · metal · 2 copies · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 356 | 0.57 | 0.75 | 40 | empty |
Compared structures
- 3UMK · X-ray structure of the E2 domain of the human amyloid precursor protein (APP) in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain A against A, TM-score 0.89
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 P05067
- Elsewhere: RCSB PDB 3UMK · PDBe 3UMK · UniProt P05067
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