Research workbench
Crystal structure of human insulin degrading enzyme in complex with iodinated insulin
Analyse Crystal structure of human insulin degrading enzyme in complex with iodinated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WC0
- Type
- protein
- Length
- 1,986 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 0.88
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 952 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 954 | 43% helix, 21% strand | P14735 |
| C, E | Insulin a chain | protein | 20 | 45% helix, 5% strand | P01308 |
| D, F | Insulin B chain | protein | 20 | 40% helix, 0% strand | P01308 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, D, B, F
- DIO · 1,4-diethylene dioxide · additive · 8 copies · chains A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.88 | 0.89 | 128 | DIO |
| 2 | 1120 | 0.88 | 0.89 | 146 | DIO |
| 3 | 1000 | 0.79 | 0.81 | 95 | empty |
| 4 | 741 | 0.79 | 0.83 | 66 | empty |
| 5 | 513 | 0.79 | 0.86 | 52 | empty |
Interfaces
7 interfaces between chains.
- B–F · 985 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 936 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 900 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 868 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 826 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 2WC0 · crystal structure of human insulin degrading enzyme in complex with iodinated insulin · the same entry in another collection · 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 2WC0 · PDBe 2WC0 · UniProt P14735 · UniProt P01308
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