MolNFT v1 · #52814 · protein
Crystal structure of human insulin-degrading enzyme in complex with insulin
2WBY: “Crystal structure of human insulin-degrading enzyme in complex with insulin”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.87). MolNFT v1 #52814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2WBY
- Type
- protein
- Length
- 1,988 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Insulin a chain; Insulin B chain
- EC
- 3.4.24.56
- UniProt
- P14735, P01308
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 957 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 954 | 44% helix, 20% strand | P14735 |
| C, E | Insulin a chain | protein | 20 | 45% helix, 5% strand | P01308 |
| D | Insulin B chain | protein | 18 | 50% helix, 6% strand | P01308 |
| F | Insulin B chain | protein | 19 | 53% helix, 5% strand | P01308 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, F
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 | 1115 | 0.87 | 0.88 | 127 | empty |
| 2 | 1012 | 0.86 | 0.87 | 120 | empty |
| 3 | 144 | 0.81 | 0.98 | 21 | empty |
| 4 | 1085 | 0.79 | 0.81 | 90 | empty |
| 5 | 655 | 0.79 | 0.84 | 60 | empty |
Interfaces
7 interfaces between chains.
- A–B · 964 Ų buried · 11 hydrogen bonds · protein-protein
- B–F · 909 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 887 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 858 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 851 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 2WBY · Crystal structure of human insulin-degrading enzyme in complex with insulin · the same entry in another collection · chain C against C, TM-score 1.00
- P14735 · AlphaFold monomer V2.0 prediction for insulin-degrading enzyme (P14735) · a predicted model of the same protein · chain A 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 P01308
- Elsewhere: RCSB PDB 2WBY · PDBe 2WBY · UniProt P14735 · UniProt P01308
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