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- PDB-1pfx: PORCINE FACTOR IXA -

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Basic information

Entry
Database: PDB / ID: 1pfx
TitlePORCINE FACTOR IXA
Components(FACTOR IXA) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HEMOPHILIA/EGF / BLOOD COAGULATION / PLASMA / SERINE PROTEASE / CALCIUM-BINDING / HYDROLASE / GLYCOPROTEIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


coagulation factor IXa / zymogen activation / blood coagulation / endopeptidase activity / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Coagulation Factor IX / Coagulation Factor IX / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site ...Coagulation Factor IX / Coagulation Factor IX / Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-like domain / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues. / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Ribbon / Few Secondary Structures / Irregular / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Coagulation factor IX
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsBrandstetter, H. / Bauer, M. / Huber, R. / Lollar, P. / Bode, W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: X-ray structure of clotting factor IXa: active site and module structure related to Xase activity and hemophilia B.
Authors: Brandstetter, H. / Bauer, M. / Huber, R. / Lollar, P. / Bode, W.
History
DepositionJul 19, 1995Processing site: BNL
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Jun 20, 2012Group: Non-polymer description
Revision 1.4Feb 27, 2013Group: Other

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: FACTOR IXA
L: FACTOR IXA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5093
Polymers43,0552
Non-polymers4541
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)128.750, 128.750, 77.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein FACTOR IXA / CHRISTMAS FACTOR


Mass: 26054.574 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PETE / Organ: BLOOD / References: UniProt: P16293, coagulation factor IXa
#2: Protein FACTOR IXA / CHRISTMAS FACTOR


Mass: 17000.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: PETE / Organ: BLOOD / References: UniProt: P16293, coagulation factor IXa
#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
Compound detailsDUE TO THE LACK OF CALCIUM IN THE CRYSTALS, GLA DOMAIN (1-46) IS MAINLY DISORDERED. BACKBONE OF C- ...DUE TO THE LACK OF CALCIUM IN THE CRYSTALS, GLA DOMAIN (1-46) IS MAINLY DISORDERED. BACKBONE OF C-TERMINAL "HYDROPHOBIC HELIX" OF THE GLA MODULE (35 - 46) IS IDENTIFIED BY CYLINDRICAL ELECTRON DENSITY; AZIMUTHAL ORIENTATION IS CONSISTENT WITH CRYSTAL PACKING.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 47 %
Crystal grow
*PLUS
pH: 6.6 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
122 %PEG60001reservoir
20.5 Msodium acetate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→8 Å / Num. obs: 10693 / % possible obs: 89.2 % / Observed criterion σ(I): 3 / Redundancy: 1.8 % / Rmerge(I) obs: 0.098
Reflection
*PLUS
Num. obs: 12050

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.198 -
obs0.198 10693
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3015 0 29 0 3044
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.01
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.87
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.64
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.87
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.64

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