Research workbench
Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-42)
Analyse Crystal structure of human insulin-degrading enzyme in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WK3
- Type
- protein
- Length
- 1,934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin degrading enzyme; Beta-amyloid protein 42
- EC
- 3.4.24.56
- UniProt
- P14735, P05067
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin degrading enzyme (EC 3.4.24.56) | protein | 958 | 44% helix, 20% strand | P14735 |
| B | Insulin degrading enzyme (EC 3.4.24.56) | protein | 956 | 44% helix, 20% strand | P14735 |
| C, D | Beta-amyloid protein 42 | protein | 10 | 0% helix, 30% strand | P05067 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1021 | 0.78 | 0.80 | 99 | empty |
| 2 | 654 | 0.78 | 0.83 | 77 | empty |
| 3 | 999 | 0.77 | 0.79 | 104 | empty |
| 4 | 1167 | 0.73 | 0.76 | 104 | empty |
| 5 | 303 | 0.68 | 0.83 | 38 | empty |
Interfaces
3 interfaces between chains.
- B–D · 980 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 931 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 874 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 2WK3 · Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-42) · 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 D against A, TM-score 0.37
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 P14735
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 2WK3 · PDBe 2WK3 · UniProt P14735 · UniProt P05067
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