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- PDB-1ksn: Crystal Structure of Human Coagulation Factor XA Complexed with FXV673 -

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Basic information

Entry
Database: PDB / ID: 1ksn
TitleCrystal Structure of Human Coagulation Factor XA Complexed with FXV673
Components(COAGULATION FACTOR XAFactor X) x 2
KeywordsHYDROLASE
Function / homology
Function and homology information


coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / Laminin / Laminin / EGF-type aspartate/asparagine hydroxylation site / EGF-like domain / 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 / 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
Chem-FXV / Coagulation factor X
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaignan, S. / Guilloteau, J.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2002
Title: Optimization of the beta-aminoester class of factor Xa inhibitors. Part 2: Identification of FXV673 as a potent and selective inhibitor with excellent In vivo anticoagulant activity.
Authors: Guertin, K.R. / Gardner, C.J. / Klein, S.I. / Zulli, A.L. / Czekaj, M. / Gong, Y. / Spada, A.P. / Cheney, D.L. / Maignan, S. / Guilloteau, J.P. / Brown, K.D. / Colussi, D.J. / Chu, V. / ...Authors: Guertin, K.R. / Gardner, C.J. / Klein, S.I. / Zulli, A.L. / Czekaj, M. / Gong, Y. / Spada, A.P. / Cheney, D.L. / Maignan, S. / Guilloteau, J.P. / Brown, K.D. / Colussi, D.J. / Chu, V. / Heran, C.L. / Morgan, S.R. / Bentley, R.G. / Dunwiddie, C.T. / Leadley, R.J. / Pauls, H.W.
History
DepositionJan 14, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAGULATION FACTOR XA
B: COAGULATION FACTOR XA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,2494
Polymers43,7612
Non-polymers4882
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-21 kcal/mol
Surface area13470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.810, 71.600, 79.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COAGULATION FACTOR XA / Factor X


Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: ACTIVATED FACTOR XA, HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#2: Protein COAGULATION FACTOR XA / Factor X


Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: FACTOR X LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FXV / METHYL-3-(4'-N-OXOPYRIDYLPHENOYL)-3-METHYL-2-(M-AMIDINOBENZYL)-PROPIONATE / FXV673 / Otamixaban


Mass: 447.506 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H27N4O4 / Comment: anticoagulant, inhibitor*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 18-20% PEG 600, 50MM MES-NAOH, 1MM RPR128515, pH 5.7, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54 Å
DetectorType: MACSCIENCE DIP100S / Detector: IMAGE PLATE / Date: Jul 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→28 Å / Num. all: 18245 / Num. obs: 15384 / % possible obs: 81.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rsym value: 0.063

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
X-PLOR98refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→28 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rwork0.223 -
all0.223 18245
obs0.223 15353
Displacement parametersBiso mean: 35.3 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2236 0 34 135 2405
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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