5LRJ

Crystal structure of the porcine carboxypeptidase B - Anabaenopeptin C complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 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:  

  • 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 ...

    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: 

    Sanofi-Aventis Deutschland GmbH, Industriepark Höchst, 65926, Frankfurt am Main, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Carboxypeptidase B
A, B, C
306Sus scrofaMutation(s): 0 
Gene Names: CPB1 (CPB)
EC: 3.4.17.2
Find proteins for P09955 (Sus scrofa)
Go to Gene View: CPB1
Go to UniProtKB:  P09955
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Anabaenopeptin C
F, G, H
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
73P
Query on 73P
F, G, H
L-PEPTIDE LINKINGC7 H14 N2 O4LYS
DLY
Query on DLY
F, G, H
D-PEPTIDE LINKINGC6 H14 N2 O2

--

73O
Query on 73O
F, G, H
L-PEPTIDE LINKINGC10 H13 N O3TYR
MAA
Query on MAA
F, G, H
L-peptide linkingC4 H9 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.152 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 124.960α = 90.00
b = 124.960β = 90.00
c = 48.120γ = 120.00
Software Package:
Software NamePurpose
CNXphasing
XSCALEdata scaling
CNXrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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