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- PDB-5pb2: Crystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-p... -

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Basic information

Entry
Database: PDB / ID: 5pb2
TitleCrystal Structure of Factor VIIa in complex with 2-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-3-ol
Components(Coagulation factor VII ...) x 2
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 / positive regulation of leukocyte chemotaxis / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / animal organ regeneration / positive regulation of blood coagulation / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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-9RP / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsStihle, M. / Mayweg, A. / Roever, S. / Rudolph, M.G.
CitationJournal: To be published
Title: Crystal Structure of a Factor VIIa complex
Authors: Mayweg, A. / Roever, S. / Rudolph, M.G.
History
DepositionNov 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2018Group: Structure summary / Category: pdbx_deposit_group / Item: _pdbx_deposit_group.group_type
Revision 1.2Nov 17, 2021Group: Database references / Derived calculations / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_struct_special_symmetry
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Coagulation factor VII light chain
C: Coagulation factor VII heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7569
Polymers35,0882
Non-polymers6687
Water6,233346
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.683, 95.683, 116.746
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
11C-860-

HOH

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Components

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Coagulation factor VII ... , 2 types, 2 molecules AC

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


Mass: 6984.911 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein Coagulation factor VII heavy chain / 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 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P08709, coagulation factor VIIa

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Non-polymers , 6 types, 353 molecules

#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-9RP / 1-phenyl-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)-1H-pyrazol-5-ol


Mass: 276.293 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H12N4O
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 346 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 16 mg/ml protein in 20mM Tris/HCl pH 8.4, 5 mM benzamidine, 0.1 M NaCl, 50 mM CaCl2 mixed 1+1 with 32-35% AMMONIUM SULPHATE, 2% PEG 4000, 0.1 M Bicine-NaOH pH 8.5, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.45→34.51 Å / Num. obs: 94122 / % possible obs: 97.8 % / Redundancy: 6.68 % / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 12.86
Reflection shellResolution: 1.45→1.55 Å / Redundancy: 4.19 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 2.03 / Rsym value: 0.506 / Rejects: 0 / % possible all: 89.3

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
SADABSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.45→33.83 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.102 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The numbering follows that of the unprocessed precursor. There is density close (2A) to C8 of the azaindole moiety indicating that a small population of the S1-group could be rotated. The ...Details: The numbering follows that of the unprocessed precursor. There is density close (2A) to C8 of the azaindole moiety indicating that a small population of the S1-group could be rotated. The water molecule bridging the S1-group with Asp398 appears mobile. The binding mode induces strained geometry in Ser423, which is an outlier in the Ramachandran plot. The main-chain GLY425-GLY427 is largely disordered, GLN426 was modelled as ALA.. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2036 4461 5 %RANDOM
Rwork0.1958 ---
obs0.1962 84967 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.4 Å2 / Biso mean: 17.747 Å2 / Biso min: 10.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.37 Å20 Å2
3---0.74 Å2
Refinement stepCycle: final / Resolution: 1.45→33.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2372 0 47 346 2765
Biso mean--31.84 33.97 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212621
X-RAY DIFFRACTIONr_bond_other_d0.0020.021803
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.973593
X-RAY DIFFRACTIONr_angle_other_deg2.6713.0074371
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.77922.655113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.07415430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1761524
X-RAY DIFFRACTIONr_chiral_restr0.0810.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212946
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02539
X-RAY DIFFRACTIONr_mcbond_it0.7761.51593
X-RAY DIFFRACTIONr_mcbond_other0.1331.5652
X-RAY DIFFRACTIONr_mcangle_it1.45522596
X-RAY DIFFRACTIONr_scbond_it1.79131028
X-RAY DIFFRACTIONr_scangle_it2.9984.5980
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 163 -
Rwork0.356 3482 -
all-3645 -
obs--52.19 %

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