Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Dihedral - D3  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 12-mer - A6B6 

Biological assembly 2 generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 18237.44 
• Atom Count: 1222 
• Residue Count: 153 
• Unique protein chains: 2

2OMH

Structure of human insulin cocrystallized with ARG-12 peptide in presence of urea

• DOI: 10.2210/pdb2OMH/pdb

• Classification: HORMONE
• Organism(s): Homo sapiens


• Deposited: 2007-01-22 Released: 2007-03-27 
• Deposition Author(s): Norrman, M., Schluckebier, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 

Literature

Structural characterization of insulin NPH formulations.

Norrman, M., Hubalek, F., Schluckebier, G.

(2007) EUR.J.PHARM.SCI. 30: 414-423

• PubMed: 17339105 
• DOI: 10.1016/j.ejps.2007.01.003
• Primary Citation of Related Structures:  
  2OMG, 2OMI


• PubMed Abstract: 
  

Insulin NPH (neutral protamine hagedorn) has for long been one of the most important therapeutic formulations for the treatment of diabetes. The protracted action profile of NPH formulations is gained from crystallizing insulin with zinc in the presence of the basic poly-arginine peptide protamine. In spite of its long history and successful use, the binding mode of the insulin-protamine complex is not known. In this study, three different systems were used to study protamine binding to insulin. In the first system, crystals of an insulin-protamine complex grown in the presence of urea and diffracting to 1.5A resolution were analyzed. In the second system, a shorter peptide consisting of 12 arginine residues was co-crystallized with insulin in order to reduce the flexibility and thereby improve the electron density of the peptide. Both systems yielded data to a significantly higher resolution than obtained previously. In addition, a third system was analyzed where crystals of insulin and protamine were grown in the absence of urea, with conditions closely resembling the pharmaceutical formulation. Data from these NPH microcrystals could for the first time be collected to 2.2A resolution at a micro focused X-ray beamline. Analysis of all three crystal forms reveal potential protamine density located close to the solvent channel leading to the centrally located zinc atoms in the insulin hexamer and support that protamine binds to insulin in a not well defined conformation.

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Organizational Affiliation: 

Diabetes Protein Engineering, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Insulin A chain	A, C, E	21	Homo sapiens	Mutation(s): 0  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Insulin B chain	B, D, F	30	Homo sapiens	Mutation(s): 0  Gene Names: INS
Find proteins for P01308 (Homo sapiens) Go to Gene View: INS Go to UniProtKB:  P01308

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
CL	B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
URE	A, C, E, F	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N
ARF	D, F	FORMAMIDE C H3 N O ZHNUHDYFZUAESO-UHFFFAOYSA-N
RCO	A, C, E	RESORCINOL 1,3-BENZENEDIOL; 1,3-DIHYDROXYBENZENE C6 H6 O2 GHMLBKRAJCXXBS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.36 Å
• R-Value Free: 0.223 
• R-Value Work: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 61.360	α = 90.00
b = 61.360	β = 90.00
c = 85.600	γ = 90.00

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-22 
• Released Date: 2007-03-27 
• Deposition Author(s): Norrman, M., Schluckebier, G.

Revision History 

• Version 1.0: 2007-03-27
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Advisory, Derived calculations, Version format compliance
• Version 1.3: 2018-03-07
  Type: Data collection