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- PDB-5par: Crystal Structure of Factor VIIa in complex with 1H-benzimidazol-... -

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Basic information

Entry
Database: PDB / ID: 5par
TitleCrystal Structure of Factor VIIa in complex with 1H-benzimidazol-2-amine
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 / 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 / response to estrogen / circadian rhythm / 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 / Laminin / 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. ...Peptidase S1A, coagulation factor VII/IX/X/C/Z / : / Coagulation factor-like, Gla domain superfamily / Laminin / Laminin / 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 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 family, serine active site. / Serine proteases, trypsin domain profile. / 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
1H-benzimidazol-2-amine / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 10, 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 / Structure summary / Category: database_2 / pdbx_deposit_group
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_deposit_group.group_description / _pdbx_deposit_group.group_title
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)36,10813
Polymers35,0882
Non-polymers1,02011
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.479, 95.479, 116.331
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-785-

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, 242 molecules

#3: Chemical
ChemComp-AX7 / 1H-benzimidazol-2-amine


Mass: 133.151 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7N3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


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


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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.78 Å3/Da / Density % sol: 67.46 % / Mosaicity: 0.95 °
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: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Apr 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 31114 / % possible obs: 96.9 % / Redundancy: 2.7 % / Rmerge(I) obs: 0.09 / Χ2: 0.997 / Net I/av σ(I): 9.871 / Net I/σ(I): 8.8 / Num. measured all: 83961
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.182.30.61929270.99592.7
2.18-2.262.40.50129661.00895
2.26-2.372.50.36730591.00297
2.37-2.492.60.31231050.98698.2
2.49-2.652.70.23131630.96499.2
2.65-2.852.70.16431431.01199.3
2.85-3.142.80.11831830.99399.4
3.14-3.592.90.07631821.00598.6
3.59-4.5230.05431791.01897.4
4.52-5030.03932070.98692.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 2.1→42.72 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.178 / SU ML: 0.111 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the numbering follows that of the unprocessed precursor four ligand molecules bound to 7a, the one in the s1 pocket being well defined.. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2195 1383 4.9 %RANDOM
Rwork0.1821 ---
obs0.184 26774 87.74 %-
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: 80 Å2 / Biso mean: 37.758 Å2 / Biso min: 32.69 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.88 Å2
Refinement stepCycle: final / Resolution: 2.1→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2376 0 65 231 2672
Biso mean--59.95 51.65 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212607
X-RAY DIFFRACTIONr_bond_other_d0.0020.021770
X-RAY DIFFRACTIONr_angle_refined_deg1.3831.9783566
X-RAY DIFFRACTIONr_angle_other_deg0.9223.0084282
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145333
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.15322.768112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88215420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2881523
X-RAY DIFFRACTIONr_chiral_restr0.0850.2384
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022911
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02529
X-RAY DIFFRACTIONr_nbd_refined0.1960.2419
X-RAY DIFFRACTIONr_nbd_other0.2030.21836
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21182
X-RAY DIFFRACTIONr_nbtor_other0.0830.21371
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2212
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0690.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.212
X-RAY DIFFRACTIONr_mcbond_it0.9511.51652
X-RAY DIFFRACTIONr_mcbond_other0.161.5649
X-RAY DIFFRACTIONr_mcangle_it1.47422559
X-RAY DIFFRACTIONr_scbond_it1.8131157
X-RAY DIFFRACTIONr_scangle_it2.7744.5996
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 84 -
Rwork0.256 1605 -
all-1689 -
obs--72.37 %

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