Experimental Data Snapshot
Starting Model:experimental
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(2013) Biochemistry 52: 295
Insulin degludec, an engineered acylated insulin, was recently reported to form a soluble depot after subcutaneous injection with a subsequent slow release of insulin and an ultralong glucose-lowering effect in excess of 40 h in humans. We describe the structure, ligand binding properties, and self-assemblies of insulin degludec using orthogonal structural methods. The protein fold adopted by insulin degludec is very similar to that of human insulin. Hexamers in the R(6) state similar to those of human insulin are observed for insulin degludec in the presence of zinc and resorcinol. However, under conditions comparable to the pharmaceutical formulation comprising zinc and phenol, insulin degludec forms finite dihexamers that are composed of hexamers in the T(3)R(3) state that interact to form an R(3)T(3)-T(3)R(3) structure. When the phenolic ligand is depleted and the solvent condition thereby mimics that of the injection site, the quaternary structure changes from dihexamers to a supramolecular structure composed of linear arrays of hundreds of hexamers in the T(6) state and an average molar mass, M(0), of 59.7 × 10(3) kg/mol. This novel concept of self-assemblies of insulin controlled by zinc and phenol provides the basis for the slow action profile of insulin degludec. To the best of our knowledge, this report for the first time describes a tight linkage between quaternary insulin structures of hexamers, dihexamers, and multihexamers and their allosteric state and its origin in the inherent propensity of the insulin hexamer for allosteric half-site reactivity.
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Biological assembly 1 assigned by authors and generated by PISA (software)
 Explore in 3D: Structure |Sequence Annotations |Electron Density |Validation Report |Ligand Interaction (IPH)
Biological assembly 2 assigned by authors and generated by PISA (software)
Macromolecule Content 
Find similar proteins by: Sequence | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| INSULIN A CHAIN | 21 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308 | |||||
PHAROS:  P01308 GTEx:  ENSG00000254647  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01308 | ||||
Sequence AnnotationsExpand | |||||
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Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| INSULIN B CHAIN | 29 | Homo sapiens | Mutation(s): 0  | ![]() | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P01308 (Homo sapiens) Explore P01308  Go to UniProtKB:  P01308 | |||||
PHAROS:  P01308 GTEx:  ENSG00000254647  | |||||
Entity Groups  | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P01308 | ||||
Sequence AnnotationsExpand | |||||
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| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| IPH Query on IPH Download Ideal Coordinates CCD File  | H [auth D] | PHENOL C6 H6 O ISWSIDIOOBJBQZ-UHFFFAOYSA-N | |||
| ZN Query on ZN Download Ideal Coordinates CCD File  | E [auth B], F [auth D] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
| CL Query on CL Download Ideal Coordinates CCD File  | G [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 79.55 | α = 90 |
| b = 79.55 | β = 90 |
| c = 38.97 | γ = 120 |
| Software Name | Purpose |
|---|---|
| REFMAC | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PHASER | phasing |
RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729.