7QAJ

ZK002 with Anti-angiogenic and Anti-inflamamtory Properties


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.200 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Isolation and characterization of ZK002, a novel dual function snake venom protein from Deinagkistrodon acutus with anti-angiogenic and anti-inflammatory properties.

Chan, B.D.Wong, W.Y.Lee, M.M.Yue, P.Y.Dai, X.Tsim, K.W.Hsiao, W.W.Li, M.Li, X.Y.Tai, W.C.

(2023) Front Pharmacol 14: 1227962-1227962

  • DOI: https://doi.org/10.3389/fphar.2023.1227962
  • Primary Citation of Related Structures:  
    7QAJ

  • PubMed Abstract: 

    Introduction: Pathological angiogenesis, the abnormal or excessive generation of blood vessels, plays an important role in many diseases including cancer, diabetic retinopathy, psoriasis, and arthritis. Additionally, increasing evidence supports the close linkage between angiogenesis and inflammation. Snake venoms are a rich natural source of biologically active molecules and carry rich potential for the discovery of anti-angiogenic and anti-inflammatory modulators. Methods: Here, we isolated and purified a novel protein, ZK002, from the venom of the snake Deinagkistrodon acutus , and investigated its anti-angiogenic and anti-inflammatory activities and mechanisms. Results: ZK002 was identified as a 30 kDa heterodimeric protein of α and β chains, which exhibited anti-angiogenic activity in various in vitro assays. Mechanistically, ZK002 inhibited activation of VEGF signaling and related mediators including eNOS, p38, LIMK, and HSP27. ZK002 also upregulated the metalloproteinase inhibitor TIMP3 and inhibited components of the VEGF-induced signaling cascade, PPP3R2 and SH2D2A. The anti-angiogenic activity of ZK002 was confirmed in multiple in vivo models. ZK002 could also inhibit the in vitro expression of pro-inflammatory cytokines, as well as in vivo inflammation in the carrageenin-induced edema rat model. Conclusion: Our findings highlight the potential for further development of ZK002 as a dual function therapeutic against diseases with involvement of pathogenic angiogenesis and chronic inflammation.


  • Organizational Affiliation

    Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Snaclec clone 2100755 betaA [auth B],
B [auth D],
C [auth F],
D [auth H]
132Deinagkistrodon acutusMutation(s): 0 
UniProt
Find proteins for Q8JIV8 (Deinagkistrodon acutus)
Explore Q8JIV8 
Go to UniProtKB:  Q8JIV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8JIV8
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Snaclec clone 2100755 alphaE [auth C],
F [auth A],
G,
H [auth E]
133Deinagkistrodon acutusMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.242 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.198 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.200 (Depositor) 
Space Group: P 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.16α = 90
b = 54.29β = 100.56
c = 107.64γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SO4Click on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other private--

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-14
    Type: Initial release
  • Version 1.1: 2023-11-01
    Changes: Data collection, Database references
  • Version 1.2: 2024-02-07
    Changes: Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary