MolNFT v1 · #66117 · protein
Crystal structure of human insulin-degrading enzyme in complex with amylin
3HGZ: “Crystal structure of human insulin-degrading enzyme in complex with amylin”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.80). MolNFT v1 #66117 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3HGZ
- Type
- protein
- Length
- 1,934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Islet amyloid polypeptide
- EC
- 3.4.24.56
- UniProt
- P14735, P10997
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 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 | 959 | 44% helix, 20% strand | P14735 |
| D | Islet amyloid polypeptide | protein | 7 | 0% helix, 29% strand | P10997 |
| E | Islet amyloid polypeptide | protein | 10 | 0% helix, 20% strand | P10997 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.80 | 0.81 | 103 | empty |
| 2 | 990 | 0.78 | 0.80 | 96 | empty |
| 3 | 1022 | 0.78 | 0.79 | 101 | empty |
| 4 | 980 | 0.76 | 0.79 | 108 | empty |
| 5 | 709 | 0.72 | 0.79 | 83 | empty |
Interfaces
3 interfaces between chains.
- A–B · 856 Ų buried · 11 hydrogen bonds · protein-protein
- B–E · 800 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 694 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 3HGZ · Crystal structure of human insulin-degrading enzyme in complex with amylin · the same entry in another collection · chain A against A, TM-score 1.00
- P10997 · AlphaFold monomer V2.0 prediction for islet amyloid polypeptide (P10997) · a predicted model of the same protein · chain D against A, TM-score 0.46
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 P10997
- Elsewhere: RCSB PDB 3HGZ · PDBe 3HGZ · UniProt P14735 · UniProt P10997
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