2WPK

factor IXa superactive triple mutant, ethylene glycol-soaked

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

Structural Basis of the Cofactor- and Substrate-Assisted Activation of Human Coagulation Factor Ixa

Zogg, T., Brandstetter, H.

(2009) Structure 17: 1669

  • DOI: 10.1016/j.str.2009.10.011
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Human coagulation factor IX serves both to maintain and to control blood coagulation. The dual function of this hemophilic factor is implemented by a tiered activation mechanism. Processed two-chain factor IXa is catalytically silent; only together w ...

    Human coagulation factor IX serves both to maintain and to control blood coagulation. The dual function of this hemophilic factor is implemented by a tiered activation mechanism. Processed two-chain factor IXa is catalytically silent; only together with its cofactor VIIIa does factor IXa form the highly potent Xase complex. The detailed mechanism of this secondary activation has remained elusive so far. Here we present the crystal structures of Xase-like factor IXa mutants with several-thousand-fold activity enhancement that mimic the secondary activation by Xase formation. The structures reveal how cofactor-triggered and substrate-assisted modulations in the factor IXa 99- and 60-loops cooperate in S4 through S2' formation, allowing for productive substrate recognition. We could further physically map and visualize a distinct communication line, along which agonists such as Ca(2+) direct their effects to the active site and vice versa.

    Organizational Affiliation: 

    Department of Molecular Biology, Division of Structural Biology, University of Salzburg, 5020 Salzburg, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR IXA LIGHT CHAIN
E
59Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Go to Gene View: F9
Go to UniProtKB:  P00740
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-PHE-PRO-ARG-CHLOROMETHYL KETONE
L
3N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COAGULATION FACTOR IXA HEAVY CHAIN
S
235Homo sapiensMutation(s): 3 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Go to Gene View: F9
Go to UniProtKB:  P00740
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
S
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO
Download SDF File 
Download CCD File 
S
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_001148
Query on PRD_001148		LBIVALIRUDIN C-terminus fragmentPeptide-like / Thrombin inhibitor

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.070α = 90.00
b = 66.530β = 90.00
c = 96.740γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
iMOSFLMdata reduction
SCALAdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2013-10-23
    Type: Other, Structure summary, Version format compliance
  • Version 1.2: 2016-12-21
    Type: Source and taxonomy
  • Version 1.3: 2017-07-05
    Type: Data collection