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- PDB-4jyu: Structure of factor VIIA in complex with the inhibitor (2R)-2-[(1... -

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Basic information

Entry
Database: PDB / ID: 4jyu
TitleStructure of factor VIIA in complex with the inhibitor (2R)-2-[(1-AMINOISOQUINOLIN-6-YL)AMINO]-2-[3-ETHOXY-4-(PROPAN-2-YLOXY)PHENYL]-N-(PHENYLSULFONYL)ETHANAMIDE
Components
  • Factor VII heavy chain
  • Factor VII light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / GLYCOPROTEIN / HYDROLASE / SERINE PROTEASE / PLASMA / BLOOD COAGULATION FACTOR / PROTEIN INHIBITOR COMPLEX / CALCIUM-BINDING / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / protein processing / Golgi lumen / circadian rhythm / response to estrogen / blood coagulation / response to estradiol / collagen-containing extracellular matrix / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / 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. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / Coagulation factor-like, Gla domain superfamily / Laminin / Coagulation Factor Xa inhibitory site / 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 / 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-1OK / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Molecular Substitution / Resolution: 1.8 Å
AuthorsWei, A. / Anumula, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Nonbenzamidine acylsulfonamide tissue factor-factor VIIa inhibitors.
Authors: Glunz, P.W. / Zhang, X. / Zou, Y. / Delucca, I. / Nirschl, A.H. / Cheng, X. / Weigelt, C.A. / Cheney, D.L. / Wei, A. / Anumula, R. / Luettgen, J.M. / Rendina, A.R. / Harpel, M. / Luo, G. / ...Authors: Glunz, P.W. / Zhang, X. / Zou, Y. / Delucca, I. / Nirschl, A.H. / Cheng, X. / Weigelt, C.A. / Cheney, D.L. / Wei, A. / Anumula, R. / Luettgen, J.M. / Rendina, A.R. / Harpel, M. / Luo, G. / Knabb, R. / Wong, P.C. / Wexler, R.R. / Priestley, E.S.
History
DepositionApr 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Factor VII light chain
L: Factor VII heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,46112
Polymers34,1342
Non-polymers1,32710
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-96 kcal/mol
Surface area12910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.200, 95.200, 117.500
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-664-

HOH

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein Factor VII light chain / Proconvertin / Serum prothrombin conversion accelerator / SPCA / Coagulation factor VII


Mass: 28103.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Factor VII heavy chain / Proconvertin / Serum prothrombin conversion accelerator / SPCA / Coagulation factor VII


Mass: 6030.827 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa

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Non-polymers , 5 types, 384 molecules

#3: Chemical ChemComp-1OK / (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-N-(phenylsulfonyl)ethanamide


Mass: 534.627 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H30N4O5S
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 3.9 Å3/Da / Density % sol: 68.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, pH 6.0, 20 mM CACL2, 17.5%(W/V) PEG 6000, vapor diffusion, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 50854 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / Biso Wilson estimate: 22.93 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 42.4
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.11.4refinement
PDB_EXTRACT3.11data extraction
HKL-2000(DENZO)data reduction
HKL-2000(SCALEPACK)data scaling
BUSTER2.11.4refinement
RefinementMethod to determine structure: Molecular Substitution / Resolution: 1.8→24.18 Å / Cor.coef. Fo:Fc: 0.9566 / Cor.coef. Fo:Fc free: 0.9485 / Occupancy max: 1 / Occupancy min: 0.3 / SU R Cruickshank DPI: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1918 2425 5.01 %RANDOM
Rwork0.175 ---
obs0.1758 48441 95.74 %-
Displacement parametersBiso max: 115.51 Å2 / Biso mean: 28.2835 Å2 / Biso min: 10.59 Å2
Baniso -1Baniso -2Baniso -3
1-1.5813 Å20 Å20 Å2
2--1.5813 Å20 Å2
3----3.1626 Å2
Refine analyzeLuzzati coordinate error obs: 0.188 Å
Refinement stepCycle: LAST / Resolution: 1.8→24.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2343 0 83 374 2800
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d845SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes47HARMONIC2
X-RAY DIFFRACTIONt_gen_planes416HARMONIC5
X-RAY DIFFRACTIONt_it2529HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion322SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance8HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3259SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2529HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3462HARMONIC21.06
X-RAY DIFFRACTIONt_omega_torsion3.97
X-RAY DIFFRACTIONt_other_torsion15.16
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2453 161 4.7 %
Rwork0.2275 3261 -
all0.2283 3422 -
obs--95.74 %

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