5BQQ | pdb_00005bqq

Human insulin with intra-chain chemical crosslink between modified B27 and B30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free: 
    0.195 (Depositor), 0.205 (DCC) 
  • R-Value Work: 
    0.161 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.163 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 5BQQ

This is version 1.2 of the entry. See complete history

Literature

Rational steering of insulin binding specificity by intra-chain chemical crosslinking.

Vikova, J.Collinsova, M.Kletvikova, E.Budesinsky, M.Kaplan, V.Zakova, L.Veverka, V.Hexnerova, R.Avino, R.J.Strakova, J.Selicharova, I.Vanek, V.Wright, D.W.Watson, C.J.Turkenburg, J.P.Brzozowski, A.M.Jiracek, J.

(2016) Sci Rep 6: 19431-19431

  • DOI: https://doi.org/10.1038/srep19431
  • Primary Citation Related Structures: 
    2N2V, 2N2W, 2N2X, 5BOQ, 5BPO, 5BQQ

  • PubMed Abstract: 

    Insulin is a key hormone of human metabolism with major therapeutic importance for both types of diabetes. New insulin analogues with more physiological profiles and better glycemic control are needed, especially analogues that preferentially bind to the metabolic B-isoform of insulin receptor (IR-B). Here, we aimed to stabilize and modulate the receptor-compatible conformation of insulin by covalent intra-chain crosslinking within its B22-B30 segment, using the Cu(I)-catalyzed Huisgen 1,3-dipolar cycloaddition reaction of azides and alkynes. This approach resulted in 14 new, systematically crosslinked insulin analogues whose structures and functions were extensively characterized and correlated. One of the analogues, containing a B26-B29 triazole bridge, was highly active in binding to both IR isoforms, with a significant preference for IR-B. Our results demonstrate the potential of chemistry-driven modulation of insulin function, also shedding new light on the functional importance of hormone's B-chain C-terminus for its IR-B specificity.


  • Organizational Affiliation
    • Institute of Organic Chemistry and Biochemistry, the Czech Academy of Sciences, v.v.i., Flemingovo n. 2, 166 10 Praha 6, Czech Republic.

Macromolecule Content 

  • Total Structure Weight: 35.83 kDa 
  • Atom Count: 2,913 
  • Modeled Residue Count: 303 
  • Deposited Residue Count: 306 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Insulin
A, C, E, G, I
A, C, E, G, I, K
21Homo 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
Insulin
B, D, F, H, J
B, D, F, H, J, L
30Homo sapiensMutation(s): 1 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IPH

Query on IPH



Download:Ideal Coordinates CCD File
M [auth A]
P [auth C]
S [auth E]
T [auth G]
U [auth H]
M [auth A],
P [auth C],
S [auth E],
T [auth G],
U [auth H],
V [auth H],
W [auth I],
X [auth J],
Y [auth J],
Z [auth K]
PHENOL
C6 H6 O
ISWSIDIOOBJBQZ-UHFFFAOYSA-N
ZN

Query on ZN



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

Query on CL



Download:Ideal Coordinates CCD File
O [auth B],
R [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
HIX
Query on HIX
B, D, F, H, J
B, D, F, H, J, L
L-PEPTIDE LINKINGC5 H8 N4 O2ALA
NVA
Query on NVA
B, D, F, H, J
B, D, F, H, J, L
L-PEPTIDE LINKINGC5 H11 N O2VAL

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.54 Å
  • R-Value Free:  0.195 (Depositor), 0.205 (DCC) 
  • R-Value Work:  0.161 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.163 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.992α = 90
b = 60.992β = 90
c = 81.919γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2024-01-10
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2025-10-01
    Changes: Derived calculations, Structure summary