1PFX

PORCINE FACTOR IXA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.

Brandstetter, H.Bauer, M.Huber, R.Lollar, P.Bode, W.

(1995) Proc.Natl.Acad.Sci.USA 92: 9796-9800


  • PubMed Abstract: 
  • Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-r ...

    Hereditary deficiency of factor IXa (fIXa), a key enzyme in blood coagulation, causes hemophilia B, a severe X chromosome-linked bleeding disorder afflicting 1 in 30,000 males; clinical studies have identified nearly 500 deleterious variants. The x-ray structure of porcine fIXa described here shows the atomic origins of the disease, while the spatial distribution of mutation sites suggests a structural model for factor X activation by phospholipid-bound fIXa and cofactor VIIIa. The 3.0-A-resolution diffraction data clearly show the structures of the serine proteinase module and the two preceding epidermal growth factor (EGF)-like modules; the N-terminal Gla module is partially disordered. The catalytic module, with covalent inhibitor D-Phe-1I-Pro-2I-Arg-3I chloromethyl ketone, most closely resembles fXa but differs significantly at several positions. Particularly noteworthy is the strained conformation of Glu-388, a residue strictly conserved in known fIXa sequences but conserved as Gly among other trypsin-like serine proteinases. Flexibility apparent in electron density together with modeling studies suggests that this may cause incomplete active site formation, even after zymogen, and hence the low catalytic activity of fIXa. The principal axes of the oblong EGF-like domains define an angle of 110 degrees, stabilized by a strictly conserved and fIX-specific interdomain salt bridge. The disorder of the Gla module, whose hydrophobic helix is apparent in electron density, can be attributed to the absence of calcium in the crystals; we have modeled the Gla module in its calcium form by using prothrombin fragment 1. The arched module arrangement agrees with fluorescence energy transfer experiments. Most hemophilic mutation sites of surface fIX residues occur on the concave surface of the bent molecule and suggest a plausible model for the membrane-bound ternary fIXa-FVIIIa-fX complex structure: fIXa and an equivalently arranged fX arch across an underlying fVIIIa subdomain from opposite sides; the stabilizing fVIIIa interactions force the catalytic modules together, completing fIXa active site formation and catalytic enhancement.


    Organizational Affiliation

    Max-Planck-Institut für Biochemie, Martinsried, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FACTOR IXA
C
235Sus scrofaMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P16293 (Sus scrofa)
Go to Gene View: F9
Go to UniProtKB:  P16293
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FACTOR IXA
L
146Sus scrofaMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P16293 (Sus scrofa)
Go to Gene View: F9
Go to UniProtKB:  P16293
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0G6
Query on 0G6

Download SDF File 
Download CCD File 
C
D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide
PPACK
C21 H34 Cl N6 O3
DVFLYEYCMMLBTQ-VSZNYVQBSA-O
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000020 (0G6)
Query on PRD_000020
CD-Phe-Pro-Arg-CH2ClPeptide-like / Inhibitor

--

Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
BHD
Query on BHD
L
L-PEPTIDE LINKINGC4 H7 N O5ASP
CGU
Query on CGU
L
L-PEPTIDE LINKINGC6 H9 N O6GLU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.750α = 90.00
b = 128.750β = 90.00
c = 77.200γ = 90.00
Software Package:
Software NamePurpose
X-PLORphasing
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-08-17
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Version format compliance
  • Version 1.3: 2012-06-20
    Type: Non-polymer description
  • Version 1.4: 2013-02-27
    Type: Other