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- Validation fo-fc coefficients (CIF - gz)
- Biological Assembly 1 (CIF - gz)
- Biological Assembly 1 (PDB - gz)
4EY1 | pdb_00004ey1
Human Insulin
- PDB DOI: https://doi.org/10.2210/pdb4EY1/pdb
- Classification: HORMONE
- Organism(s): Homo sapiens
- Mutation(s): No
- Deposited: 2012-05-01 Released: 2013-05-01
- Deposition Author(s): Favero-Retto, M.P., Palmieri, L.C., Lima, L.M.T.R.
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.47 Å
- R-Value Free: 0.219 (Depositor), 0.227 (DCC)
- R-Value Work: 0.160 (Depositor), 0.173 (DCC)
- R-Value Observed: 0.164 (Depositor)
wwPDB Validation 3D Report Full Report
- 👁 Image
Download Mendeley
Structural meta-analysis of regular human insulin in pharmaceutical formulations.
Favero-Retto, M.P., Palmieri, L.C., Souza, T.A., Almeida, F.C., Lima, L.M.(2013) Eur J Pharm Biopharm 85: 1112-1121
- PubMed: 23692694 Search on PubMed
- DOI: https://doi.org/10.1016/j.ejpb.2013.05.005
- Primary Citation Related Structures:
4EWW, 4EWX, 4EWZ, 4EX0, 4EX1, 4EXX, 4EY1, 4EY9, 4EYD, 4EYN, 4EYP, 4F0N, 4F0O, 4F1A, 4F1B, 4F1C, 4F1D, 4F1F, 4F1G, 4F4T, 4F4V, 4F51, 4F8F, 4FG3 - PubMed Abstract:
We have studied regular acting, wild-type human insulin at potency of 100 U/mL from four different pharmaceutical products directly from their final finished formulation by the combined use of mass spectrometry (MS), dynamic light scattering (DLS), small-angle X-ray scattering (SAXS), nuclear magnetic resonance (NMR), and single-crystal protein crystallography (PX). All products showed similar oligomeric assembly in solution as judged by DLS and SAXS measurements. The NMR spectra were compatible with well folded proteins, showing close conformational identity for the human insulin in the four products. Crystallographic assays conducted with the final formulated products resulted in all insulin crystals belonging to the R3 space group with two a dimer in the asymmetric unit, both with the B-chain in the T configuration. Meta-analysis of the 24 crystal structures solved from the four distinct insulin products revealed close similarity between them regardless of variables such as biological origin, product batch, country origin of the product, and analytical approach, revealing a low conformational variability for the converging insulin structural ensemble. We propose the use of MS, SAXS, NMR fingerprint, and PX as a precise chemical and structural proof of folding identity of regular insulin in the final, formulated product.
- School of Pharmacy, Federal University of Rio de Janeiro - UFRJ, Rio de Janeiro, Brazil; Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil; Brazilian National Institute of Traumatology and Orthopedics (INTO), Rio de Janeiro, Brazil.
Organizational Affiliation:
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZN)
Explore in 3D: Structure | Sequence Annotations | Electron Density | Validation Report | Ligand Interaction (ZN)
Global Symmetry: Dihedral - D3 (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A6B6
Pseudo Symmetry: Cyclic - C3 (Explore in 3D)
Pseudo Stoichiometry: Hetero 12-mer - A6B3C3
Find Similar Assemblies
Biological assembly 1 assigned by authors and generated by PISA (software)
Macromolecule Content
- Total Structure Weight: 11.84 kDa
- Atom Count: 968
- Modeled Residue Count: 102
- Deposited Residue Count: 102
- Unique protein chains: 2
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 | 👁 Image | |
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 | |||||
| |||||
Entity ID: 2 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Insulin B chain | 30 | Homo sapiens | Mutation(s): 0 | 👁 Image | |
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 | |||||
| |||||
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ZN Query on ZN Download Ideal Coordinates CCD File | E [auth B], G [auth D] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | 👁 Image | ||
| CL Query on CL Download Ideal Coordinates CCD File | F [auth B], H [auth D] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | 👁 Image | ||
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.47 Å
- R-Value Free: 0.219 (Depositor), 0.227 (DCC)
- R-Value Work: 0.160 (Depositor), 0.173 (DCC)
- R-Value Observed: 0.164 (Depositor)
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 80.86 | α = 90 |
| b = 80.86 | β = 90 |
| c = 33.17 | γ = 120 |
| Software Name | Purpose |
|---|---|
| MOSFLM | data reduction |
| SCALA | data scaling |
| PHASER | phasing |
| REFMAC | refinement |
| PDB_EXTRACT | data extraction |
| MAR345 | data collection |
Deposition Data
- Released Date: 2013-05-01 Deposition Author(s): Favero-Retto, M.P., Palmieri, L.C., Lima, L.M.T.R.
Revision History (Full details and data files)
- Version 1.0: 2013-05-01
Type: Initial release - Version 1.1: 2013-06-12
Changes: Database references - Version 1.2: 2013-12-18
Changes: Database references - Version 1.3: 2017-11-15
Changes: Refinement description - Version 1.4: 2024-10-16
Changes: Data collection, Database references, Derived calculations, Structure summary
