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 4EY9|pdb_00004ey9

Human Insulin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.255 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.177 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.182 (Depositor) 

wwPDB Validation  3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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

  • PubMed23692694 Search on PubMed
  • DOI: https://doi.org/10.1016/j.ejpb.2013.05.005
  • Primary Citation of 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.


  • Organizational Affiliation
    • 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.
Biological Assembly 1  

 Explore in 3DStructure |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)

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Macromolecule Content 

  • Total Structure Weight: 11.84 kDa 
  • Atom Count: 1,027 
  • Modeled Residue Count: 102 
  • Deposited Residue Count: 102 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin A chain21Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin B chain30Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01308
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B],
G [auth D]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
F [auth B],
H [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.255 (Depositor), 0.266 (DCC) 
  • R-Value Work: 0.177 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.182 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.78α = 90
b = 80.78β = 90
c = 33.17γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary
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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.


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