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- PDB-4jzd: Structure of factor VIIA in complex with the inhibitor 2-{2-[(4-c... -

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Basic information

Entry
Database: PDB / ID: 4jzd
TitleStructure of factor VIIA in complex with the inhibitor 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid
Components
  • Factor VIIa (Heavy Chain)
  • Factor VIIa (Light Chain)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / glycoprotein / 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 / signaling receptor binding / serine-type endopeptidase activity / 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 / 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-1NJ / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsJacobson, B.L. / Anumula, R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Discovery of nonbenzamidine factor VIIa inhibitors using a biaryl acid scaffold.
Authors: Bolton, S.A. / Sutton, J.C. / Anumula, R. / Bisacchi, G.S. / Jacobson, B. / Slusarchyk, W.A. / Treuner, U.D. / Wu, S.C. / Zhao, G. / Pi, Z. / Sheriff, S. / Smirk, R.A. / Bisaha, S. / Cheney, ...Authors: Bolton, S.A. / Sutton, J.C. / Anumula, R. / Bisacchi, G.S. / Jacobson, B. / Slusarchyk, W.A. / Treuner, U.D. / Wu, S.C. / Zhao, G. / Pi, Z. / Sheriff, S. / Smirk, R.A. / Bisaha, S. / Cheney, D.L. / Wei, A. / Schumacher, W.A. / Hartl, K.S. / Liu, E. / Zahler, R. / Seiler, S.M.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name / _software.version
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Factor VIIa (Heavy Chain)
L: Factor VIIa (Light Chain)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,91012
Polymers34,1342
Non-polymers1,77610
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-96 kcal/mol
Surface area14410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.830, 94.830, 118.490
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-654-

HOH

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Components

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Protein , 2 types, 2 molecules HL

#1: Protein Factor VIIa (Heavy Chain) / Factor VII heavy chain / Activated Factor VIIA Heavy Chain / Coagulation factor VII / Proconvertin ...Factor VII heavy chain / Activated Factor VIIA Heavy Chain / Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: UNP residues 213-466
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 VIIa (Light Chain) / Factor VII light chain / Coagulation factor VII / Proconvertin / Serum prothrombin conversion ...Factor VII light chain / Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 6030.827 Da / Num. of mol.: 1 / Fragment: UNP residues 150-204
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, 307 molecules

#3: Chemical ChemComp-1NJ / 2-{2-[(4-carbamimidoylphenyl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid


Mass: 533.576 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N5O6
#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 / Sulfate


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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 68.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 100 mM bicine, pH 9.0, 1.4-1.9 M lithium sulfate, 5% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 / Wavelength: 1.1 Å
DetectorType: BRANDEIS 4 / Detector: CCD / Date: Sep 20, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.198→24.679 Å / Num. obs: 28001 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 24.8
Reflection shellResolution: 2.198→2.38 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 8.1 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTBUSTER 2.9.4refinement
PDB_EXTRACT3.11data extraction
DENZO(DENZO)data reduction
SCALEPACK(DENZO)data scaling
BUSTER2.9.4refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1DAN

1dan


Resolution: 2.2→24.679 Å / Cor.coef. Fo:Fc: 0.9486 / Cor.coef. Fo:Fc free: 0.9342 / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.143 / SU Rfree Cruickshank DPI: 0.136
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2801. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=6. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=CA GOL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=2801. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=6. NUMBER TREATED BY BAD NON-BONDED CONTACTS=1.
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1218 4.35 %RANDOM
Rwork0.1643 ---
obs0.1657 27973 99.68 %-
Displacement parametersBiso max: 114.96 Å2 / Biso mean: 27.0992 Å2 / Biso min: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.2625 Å20 Å20 Å2
2--1.2625 Å20 Å2
3----2.5251 Å2
Refine analyzeLuzzati coordinate error obs: 0.194 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.679 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 115 297 2788
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d833SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes431HARMONIC5
X-RAY DIFFRACTIONt_it2574HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion316SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3108SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2574HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3519HARMONIC21.05
X-RAY DIFFRACTIONt_omega_torsion3.84
X-RAY DIFFRACTIONt_other_torsion15.28
LS refinement shellResolution: 2.2→2.28 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2189 134 4.8 %
Rwork0.1749 2659 -
all0.177 2793 -
obs--99.68 %

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