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- PDB-5pb0: Crystal Structure of Factor VIIa in complex with 2-(4-ethoxy-3-me... -

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Basic information

Entry
Database: PDB / ID: 5pb0
TitleCrystal Structure of Factor VIIa in complex with 2-(4-ethoxy-3-methoxyphenyl)-2-(isoquinolin-6-ylamino)acetic acid
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 growth hormone / response to cholesterol / 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 / 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
Chem-7LX / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.98 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 1.4Oct 23, 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
B: Coagulation factor VII heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,15913
Polymers35,0882
Non-polymers1,07111
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.272, 95.272, 116.071
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
11B-874-

HOH

21B-893-

HOH

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Components

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

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


Mass: 6984.911 Da / Num. of mol.: 1 / Fragment: FACTOR VII RESIDUES 148-466
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 / Fragment: FACTOR VII RESIDUES 148-466
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, 366 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-7LX / (2~{R})-2-(4-ethoxy-3-methoxy-phenyl)-2-(isoquinolin-6-ylamino)ethanoic acid / 2-(4-ethoxy-3-methoxyphenyl)-2-(isoquinolin-6-ylamino)acetic acid


Mass: 352.384 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N2O4
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.76 Å3/Da / Density % sol: 67.24 % / Mosaicity: 0.538 °
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: Feb 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 37699 / % possible obs: 98.7 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.1 / Χ2: 1.006 / Net I/av σ(I): 23.194 / Net I/σ(I): 9.6 / Num. measured all: 428795
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.98-2.057.90.60332501.07286.9
2.05-2.1311.40.43537450.956100
2.13-2.2311.50.35737570.977100
2.23-2.3511.60.27737711.012100
2.35-2.4911.80.2337631.023100
2.49-2.6911.80.17437951.015100
2.69-2.9611.90.12738011.014100
2.96-3.3911.90.08338411.013100
3.39-4.2611.90.0638861.016100
4.26-5011.40.04440900.98599.7

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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: 1.98→49.57 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.476 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the numbering follows that of the unprocessed precursor since insertion codes are not accepted by most programs and distinction between light and heavy chains seems cumbersome. the R- ...Details: the numbering follows that of the unprocessed precursor since insertion codes are not accepted by most programs and distinction between light and heavy chains seems cumbersome. the R-enantiomer is bound exclusively ARG A 204 ILE A 213 gap ALA A 375 SER A 380 gap. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1931 1795 5 %RANDOM
Rwork0.1675 ---
obs0.1688 34095 94.73 %-
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: 25.314 Å2 / Biso min: 18.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.3 Å20 Å2
3---0.6 Å2
Refinement stepCycle: final / Resolution: 1.98→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2363 0 61 355 2779
Biso mean--49.09 42 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212571
X-RAY DIFFRACTIONr_bond_other_d0.0020.021742
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9763521
X-RAY DIFFRACTIONr_angle_other_deg0.9193.0094221
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2595331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.62322.87108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.02115416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.9491521
X-RAY DIFFRACTIONr_chiral_restr0.090.2383
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022857
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02518
X-RAY DIFFRACTIONr_nbd_refined0.2010.2444
X-RAY DIFFRACTIONr_nbd_other0.2080.21843
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21166
X-RAY DIFFRACTIONr_nbtor_other0.0810.21384
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2300
X-RAY DIFFRACTIONr_metal_ion_refined0.0920.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0740.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2660.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.223
X-RAY DIFFRACTIONr_mcbond_it1.0681.51628
X-RAY DIFFRACTIONr_mcbond_other0.2071.5643
X-RAY DIFFRACTIONr_mcangle_it1.54622539
X-RAY DIFFRACTIONr_scbond_it2.12431124
X-RAY DIFFRACTIONr_scangle_it3.3214.5970
LS refinement shellResolution: 1.979→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 109 -
Rwork0.218 1994 -
all-2103 -
obs--76.42 %

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