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Structure of cysteine-free human insulin degrading enzyme in complex with macrocyclic inhibitor
Analyse Structure of cysteine-free 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
- 4LTE
- Type
- protein
- Length
- 1,912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme; Macrocyclic inhibitor
- EC
- 3.4.24.56
- UniProt
- P14735
- Ligands
- LYN, FUM, ZN
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 954 | 44% helix, 20% strand | P14735 |
| M, N | Macrocyclic inhibitor | protein | 2 | 0% helix, 0% strand | — |
Ligands and binding sites
- LYN · 2,6-diamino-hexanoic acid amide · ligand · 2 copies · chains A, M, B, N
- FUM · Fumaric acid · ligand · 2 copies · chains A, M, B, N
- ZN · Zinc ion · metal · 2 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.84 | 0.85 | 105 | empty |
| 2 | 520 | 0.72 | 0.81 | 60 | empty |
| 3 | 412 | 0.70 | 0.82 | 67 | empty |
| 4 | 395 | 0.66 | 0.80 | 41 | empty |
| 5 | 244 | 0.65 | 0.82 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1548 Ų buried · 17 hydrogen bonds · protein-protein
- A–M · 420 Ų buried · 2 hydrogen bonds · protein-protein
- B–N · 413 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4LTE · Structure of Cysteine-free Human Insulin Degrading Enzyme in Complex with Macrocyclic… · the same entry in another collection · chain M against M, 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
- Elsewhere: RCSB PDB 4LTE · PDBe 4LTE · UniProt P14735
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