Research workbench
Crystal structure analysis of Fab-bound human insulin degrading enzyme (ide) in complex with amyloid-beta (1-40)
Analyse Crystal structure analysis of Fab-bound human insulin degrading enzyme (ide) in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M1C
- Type
- protein
- Length
- 2,692 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Fab-bound ide, heavy chain; Fab-bound ide, light chain; Amyloid…
- EC
- 3.4.24.56
- UniProt
- P14735, P05067
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 30% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 957 | 40% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 952 | 41% helix, 18% strand | P14735 |
| C | Fab-bound ide, heavy chain | protein | 205 | 3% helix, 50% strand | — |
| D | Fab-bound ide, light chain | protein | 175 | 2% helix, 39% strand | — |
| E | Fab-bound ide, heavy chain | protein | 206 | 3% helix, 41% strand | — |
| F | Fab-bound ide, light chain | protein | 184 | 2% helix, 39% strand | — |
| G | Amyloid beta A4 protein | protein | 10 | 0% helix, 20% strand | P05067 |
| H | Amyloid beta A4 protein | protein | 3 | 0% helix, 0% strand | P05067 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, G, 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 999 | 0.86 | 0.87 | 86 | empty |
| 2 | 750 | 0.79 | 0.83 | 76 | empty |
| 3 | 802 | 0.75 | 0.79 | 98 | empty |
| 4 | 437 | 0.71 | 0.82 | 64 | empty |
| 5 | 253 | 0.67 | 0.83 | 30 | empty |
Interfaces
9 interfaces between chains.
- C–D · 1978 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1822 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1415 Ų buried · 18 hydrogen bonds · protein-protein
- A–G · 880 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 4M1C · Crystal Structure Analysis of Fab-Bound Human Insulin Degrading Enzyme (IDE) in Complex… · the same entry in another collection · chain H against H, TM-score 1.00
- P05067 · AlphaFold monomer V2.0 prediction for amyloid-beta precursor protein (P05067) · a predicted model of the same protein · chain H 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
- Every structure of UniProt P05067
- Elsewhere: RCSB PDB 4M1C · PDBe 4M1C · UniProt P14735 · UniProt P05067
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