2DOI

The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 

Starting Model: experimental
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This is version 1.6 of the entry. See complete history


Literature

X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcal surface protein PAM

Cnudde, S.E.Prorok, M.Castellino, F.J.Geiger, J.H.

(2006) Biochemistry 45: 11052-11060

  • DOI: https://doi.org/10.1021/bi060914j
  • Primary Citation of Related Structures:  
    2DOH, 2DOI

  • PubMed Abstract: 

    The crystal structure of the human Pg-derived angiogenesis inhibitor, angiostatin, complexed to VEK-30, a peptide from the group A streptococcal surface protein, PAM, was determined and refined to 2.3 A resolution. This is the first structure of angiostatin bound to a ligand and provides a model of the interaction between Pg and streptococcal-derived pathogenic proteins. VEK-30 contains a "through-space isostere" for C-terminal lysine, wherein Arg and Glu side chains, separated by one helical turn, bind within the bipolar angiostatin kringle 2 (K2) domain lysine-binding site. VEK-30 also makes several contacts with K2 residues that exist outside of the canonical LBS and are not conserved among the other Pg kringles, thus providing a molecular basis for the selectivity of VEK-30 for K2. The structure also shows that Pg kringle domains undergo significant structural rearrangement relative to one another and reveals dimerization between two molecules of angiostatin and VEK-30 related by crystallographic symmetry. This dimerization, which exists only in the crystal structure, is consistent with the parallel coiled-coil full-length PAM dimer expected from sequence similarities and homology modeling.


  • Organizational Affiliation

    Department of Biochemistry, Michigan State University, East Lansing, Michigan 48824, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
AngiostatinA [auth X],
C [auth A]
234Homo sapiensMutation(s): 1 
Gene Names: PLG
EC: 3.4.21.7
UniProt & NIH Common Fund Data Resources
Find proteins for P00747 (Homo sapiens)
Explore P00747 
Go to UniProtKB:  P00747
PHAROS:  P00747
GTEx:  ENSG00000122194 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00747
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Plasminogen-binding group A streptococcal M-like protein PAMB [auth C],
D [auth B]
30N/AMutation(s): 0 
UniProt
Find proteins for P49054 (Streptococcus pyogenes)
Explore P49054 
Go to UniProtKB:  P49054
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49054
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.202 
  • R-Value Observed: 0.202 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.467α = 90
b = 58.467β = 90
c = 389.146γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references
  • Version 1.5: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.6: 2024-10-16
    Changes: Structure summary