Research workbench
Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40)
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
- 2G47
- Type
- protein
- Length
- 1,951 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Amyloid protein beta A4
- EC
- 3.4.24.56
- UniProt
- P14735
- Pockets
- 20 · best druggability 0.87
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 | 964 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 965 | 44% helix, 20% strand | P14735 |
| C, D | Amyloid protein beta A4 | protein | 11 | 0% helix, 27% strand | — |
Ligands and binding sites
- DIO · 1,4-diethylene dioxide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 960 | 0.87 | 0.88 | 114 | empty |
| 2 | 848 | 0.78 | 0.81 | 103 | DIO |
| 3 | 702 | 0.76 | 0.81 | 76 | DIO |
| 4 | 441 | 0.73 | 0.82 | 41 | empty |
| 5 | 427 | 0.71 | 0.82 | 45 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1501 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 987 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 957 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 2G47 · Crystal structure of human insulin-degrading enzyme in complex with amyloid-beta (1-40) · the same entry in another collection · chain A against A, TM-score 1.00
- P14735 · AlphaFold monomer V2.0 prediction for insulin-degrading enzyme (P14735) · a predicted model of the same protein · chain B against A, TM-score 1.00
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
- Elsewhere: RCSB PDB 2G47 · PDBe 2G47 · UniProt P14735
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