Research workbench
Structure of cystein free insulin degrading enzyme with compound BDM41671 ((S)-2-{2-[carboxymethyl-(3-phenyl-propyl)-amino]- acetylamino}-3-(1H-imidazol-4-yl)-propionic acid methyl ester)
Analyse Structure of cystein free insulin degrading enzyme with compound BDM41671… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DWK
- Type
- protein
- Length
- 1,910 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Insulin-degrading enzyme
- EC
- 3.4.24.56
- UniProt
- P14735
- Ligands
- MGK, ZN
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 955 | 44% helix, 20% strand | P14735 |
| B | Insulin-degrading enzyme (EC 3.4.24.56) | protein | 955 | 45% helix, 20% strand | P14735 |
Ligands and binding sites
- MGK · methyl N-(carboxymethyl)-N-(3-phenylpropyl)glycyl-L-histidinate · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1115 | 0.79 | 0.81 | 99 | empty |
| 2 | 541 | 0.73 | 0.81 | 72 | empty |
| 3 | 503 | 0.72 | 0.81 | 73 | empty |
| 4 | 499 | 0.68 | 0.79 | 67 | empty |
| 5 | 353 | 0.67 | 0.81 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 915 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4DWK · Structure of cystein free insulin degrading enzyme with compound bdm41671… · 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
- Elsewhere: RCSB PDB 4DWK · PDBe 4DWK · UniProt P14735
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