1UZ9 | pdb_00001uz9

Crystallographic and solution studies of N-lithocholyl insulin: a new generation of prolonged-acting insulins.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.206 (Depositor) 
  • R-Value Work: 
    0.179 (Depositor) 
  • R-Value Observed: 
    0.180 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 1UZ9

This is version 1.4 of the entry. See complete history

Literature

Crystallographic and Solution Studies of N-Lithocholyl Insulin: A New Generation of Prolonged-Acting Human Insulins

Whittingham, J.L.Jonassen, I.Havelund, S.Roberts, S.M.Dodson, E.J.Verma, C.S.Wilkinson, A.J.Dodson, G.G.

(2004) Biochemistry 43: 5987

  • DOI: https://doi.org/10.1021/bi036163s
  • Primary Citation Related Structures: 
    1UZ9

  • PubMed Abstract: 

    The addition of specific bulky hydrophobic groups to the insulin molecule provides it with affinity for circulating serum albumin and enables it to form soluble macromolecular complexes at the site of subcutaneous injection, thereby securing slow absorption of the insulin analogue into the blood stream and prolonging its half-life once there. N-Lithocholic acid acylated insulin [Lys(B29)-lithocholyl des-(B30) human insulin] has been crystallized and the structure determined by X-ray crystallography at 1.6 A resolution to explore the molecular basis of its assembly. The unit cell in the crystal consists of an insulin hexamer containing two zinc ions, with two m-cresol molecules bound at each dimer-dimer interface stabilizing an R(6) conformation. Six covalently bound lithocholyl groups are arranged symmetrically around the outside of the hexamer. These form specific van der Waals and hydrogen-bonding interactions at the interfaces between neighboring hexamers, possibly representing the kinds of interactions which occur in the soluble aggregates at the site of injection. Comparison with an equivalent nonderivatized native insulin hexamer shows that the addition of the lithocholyl group disrupts neither the important conformational features of the insulin molecule nor its hexamer-forming ability. Indeed, binding studies show that the affinity of N-lithocholyl insulin for the human insulin receptor is not significantly diminished.


  • Organizational Affiliation
    • Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5YW, UK.

Macromolecule Content 

  • Total Structure Weight: 6.43 kDa 
  • Atom Count: 500 
  • Modeled Residue Count: 49 
  • Deposited Residue Count: 50 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
INSULIN21Homo 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
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
INSULIN29Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UZ9

Query on UZ9



Download:Ideal Coordinates CCD File
D [auth B](2S)-2-AMINO-6-({(4R)-4-[(10R,13S)-10,13-DIMETHYL-3-OXOHEXADECAHYDRO-1H-CYCLOPENTA[A]PHENANTHREN-17-YL]PENTANOYL}AMINO)HEXANOIC ACID
C30 H50 N2 O4
NZNFUUCLWNSFAF-HLKVRRRCSA-N
CRS

Query on CRS



Download:Ideal Coordinates CCD File
C [auth A]M-CRESOL
C7 H8 O
RLSSMJSEOOYNOY-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
F [auth B]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.206 (Depositor) 
  • R-Value Work:  0.179 (Depositor) 
  • R-Value Observed: 0.180 (Depositor) 
Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.79α = 90
b = 51.79β = 90
c = 68.34γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-03
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary