5LRJ

Crystal structure of the porcine carboxypeptidase B - Anabaenopeptin C complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Isolation, Co-Crystallization and Structure-Based Characterization of Anabaenopeptins as Highly Potent Inhibitors of Activated Thrombin Activatable Fibrinolysis Inhibitor (TAFIa).

Schreuder, H.Liesum, A.Lonze, P.Stump, H.Hoffmann, H.Schiell, M.Kurz, M.Toti, L.Bauer, A.Kallus, C.Klemke-Jahn, C.Czech, J.Kramer, D.Enke, H.Niedermeyer, T.H.Morrison, V.Kumar, V.Bronstrup, M.

(2016) Sci Rep 6: 32958-32958

  • DOI: 10.1038/srep32958
  • Primary Citation of Related Structures:  
    5LRK, 5LRG, 5LRJ

  • PubMed Abstract: 
  • Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis ...

    Mature thrombin activatable fibrinolysis inhibitor (TAFIa) is a carboxypeptidase that stabilizes fibrin clots by removing C-terminal arginines and lysines from partially degraded fibrin. Inhibition of TAFIa stimulates the degradation of fibrin clots and may help to prevent thrombosis. Applying a lead finding approach based on literature-mining, we discovered that anabaenopeptins, cyclic peptides produced by cyanobacteria, were potent inhibitors of TAFIa with IC50 values as low as 1.5 nM. We describe the isolation and structure elucidation of 20 anabaenopeptins, including 13 novel congeners, as well as their pronounced structure-activity relationships (SAR) with respect to inhibition of TAFIa. Crystal structures of the anabaenopeptins B, C and F bound to the surrogate protease carboxypeptidase B revealed the binding modes of these large (~850 Da) compounds in detail and explained the observed SAR, i.e. the strong dependence of the potency on a basic (Arg, Lys) exocyclic residue that addressed the S1' binding pocket, and a broad tolerance towards substitutions in the pentacyclic ring that acted as a plug of the active site.


    Organizational Affiliation

    Department of Chemical Biology, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Carboxypeptidase BA, B, C306Sus scrofaMutation(s): 0 
Gene Names: CPB1CPB
EC: 3.4.17.2
Find proteins for P09955 (Sus scrofa)
Explore P09955 
Go to UniProtKB:  P09955
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Anabaenopeptin CD [auth F], E [auth G], F [auth H]6Planktothrix rubescensMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
G [auth A], H [auth B], I [auth C]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
73O
Query on 73O
D [auth F], E [auth G], F [auth H]L-PEPTIDE LINKINGC10 H13 N O3TYR
73P
Query on 73P
D [auth F], E [auth G], F [auth H]L-PEPTIDE LINKINGC7 H14 N2 O4LYS
MAA
Query on MAA
D [auth F], E [auth G], F [auth H]L-PEPTIDE LINKINGC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.152 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 124.96α = 90
b = 124.96β = 90
c = 48.12γ = 120
Software Package:
Software NamePurpose
CNXrefinement
XDSdata reduction
XSCALEdata scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release