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- PDB-8qod: CRYSTAL STRUCTURE OF FVIIA IN COMPLEX WITH A BENZAMIDINE-BASED IN... -

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Basic information

Entry
Database: PDB / ID: 8qod
TitleCRYSTAL STRUCTURE OF FVIIA IN COMPLEX WITH A BENZAMIDINE-BASED INHIBITOR
Components
  • Coagulation factor VII
  • Factor VII light chain
  • Tissue factor
KeywordsBLOOD CLOTTING / Inhibitor complex
Function / homology
Function and homology information


activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / serine-type peptidase complex / response to carbon dioxide ...activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to genistein / serine-type peptidase complex / response to carbon dioxide / response to vitamin K / response to thyroxine / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / NGF-stimulated transcription / response to cholesterol / cytokine receptor activity / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of endothelial cell apoptotic process / positive regulation of blood coagulation / positive regulation of TOR signaling / animal organ regeneration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / positive regulation of interleukin-8 production / cytokine-mediated signaling pathway / protein processing / phospholipid binding / Golgi lumen / response to estrogen / circadian rhythm / positive regulation of angiogenesis / blood coagulation / response to estradiol / protease binding / : / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane
Similarity search - Function
Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily ...Tissue factor / Tissue factor, conserved site / Tissue factor signature. / Interferon/interleukin receptor domain / Interferon-alpha/beta receptor, fibronectin type III / : / Tissue factor / Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Coagulation Factor Xa inhibitory site / 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 1. / EGF-like domain signature 2. / EGF-like domain / Fibronectin type III / Fibronectin type III superfamily / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
alpha-L-fucopyranose / alpha-D-glucopyranose / : / Coagulation factor VII / Tissue factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.573 Å
AuthorsSchreuder, H.A. / Liesum, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To be published
Title: Crystallography and molecular simulations capture S1 pocket collapse in allosteric regulation of factor VIIa and other serine proteases.
Authors: Tesmer, L. / Hans Matter, H. / Klingler, O. / Schudok, M. / Hessler, G. / Mehdipour, A.R. / Guessregen, S. / Hummer, G. / Schreuder, H.A.
History
DepositionSep 28, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Factor VII light chain
B: Coagulation factor VII
C: Tissue factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,84413
Polymers71,7053
Non-polymers1,13910
Water19,6721092
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: factor VIIA - tissue factor complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7170 Å2
ΔGint-83 kcal/mol
Surface area27430 Å2
Unit cell
Length a, b, c (Å)69.811, 81.51, 125.498
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 3 types, 3 molecules ABC

#1: Protein Factor VII light chain


Mass: 16303.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell line (production host): BHK/VP16 / Production host: Cricetinae (hamsters) / References: UniProt: P08709
#2: Protein Coagulation factor VII / Proconvertin / Serum prothrombin conversion accelerator / SPCA


Mass: 28103.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Cell line (production host): BHK/VP16 / Production host: Cricetinae (hamsters) / References: UniProt: P08709, coagulation factor VIIa
#3: Protein Tissue factor / TF / Coagulation factor III / Thromboplastin


Mass: 27297.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Escherichia coli (E. coli) / References: UniProt: P13726

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Sugars , 2 types, 2 molecules

#6: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 1100 molecules

#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-WIZ / 3-[2-bromanyl-4-[(1~{S})-1-[[3-[(4-carbamimidoylphenyl)amino]-3-oxidanylidene-propanoyl]amino]ethyl]phenoxy]benzoic acid


Mass: 539.378 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H23BrN4O5 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1092 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: The VIIa/sTF complex was crystallized using the sitting drop or the hanging drop vapor diffusion method. Specifically, the protein drop contained 4 mg/ml VIIa/sTF complex, 20 mm Tris-HCl, pH ...Details: The VIIa/sTF complex was crystallized using the sitting drop or the hanging drop vapor diffusion method. Specifically, the protein drop contained 4 mg/ml VIIa/sTF complex, 20 mm Tris-HCl, pH 7.5, 200 mm NaCl, 10 mm CaCl2, and 10 mm pAB or 10 mm benzamidine, whereas the reservoir solution contained 16-22% PEG 4000, 100 mm MgCl2, and 20 mm BisTris, pH 6.5. Drops were prepared by mixing 2 ul of protein solution with 2 ul of reservoir solution at 20 C. Crystals appeared within 7 days and were allowed to grow up to 14-20 days before being flash-frozen without additional cryoprotectant.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.573→68.357 Å / Num. obs: 75314 / % possible obs: 75.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 21.6
Reflection shellResolution: 1.573→1.715 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.582 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3767 / CC1/2: 0.61 / Rsym value: 0.582 / % possible all: 16.8

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Processing

Software
NameVersionClassification
BUSTER2.11.8refinement
autoPROCdata reduction
XDSMar 15, 201data reduction
autoPROC1.1.7data scaling
Aimlessdata scaling
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.573→22.88 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU R Cruickshank DPI: 0.106 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.123 / SU Rfree Blow DPI: 0.114 / SU Rfree Cruickshank DPI: 0.104
RfactorNum. reflection% reflectionSelection details
Rfree0.2143 3782 -RANDOM
Rwork0.1815 ---
obs0.1832 75288 75.4 %-
Displacement parametersBiso mean: 28.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.2241 Å20 Å20 Å2
2--0.3759 Å20 Å2
3----0.1518 Å2
Refine analyzeLuzzati coordinate error obs: 0.21 Å
Refinement stepCycle: LAST / Resolution: 1.573→22.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4694 0 63 1092 5849
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0084962HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.976766HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1667SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes868HARMONIC5
X-RAY DIFFRACTIONt_it4962HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion629SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact5504SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion4.13
X-RAY DIFFRACTIONt_other_torsion15.5
LS refinement shellResolution: 1.573→1.67 Å
RfactorNum. reflection% reflection
Rfree0.3398 69 -
Rwork0.2777 --
obs--9.52 %

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