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- PDB-5pae: Crystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N... -

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Basic information

Entry
Database: PDB / ID: 5pae
TitleCrystal Structure of Factor VIIa in complex with (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]propanamide
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
Chem-7YA / 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 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: Advisory / Database references / Structure summary
Category: database_2 / pdbx_deposit_group / pdbx_unobs_or_zero_occ_atoms
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)36,17011
Polymers35,0882
Non-polymers1,0829
Water6,774376
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.270, 95.270, 116.710
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-889-

HOH

21B-902-

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
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 , 5 types, 385 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#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-7YA / (2S)-2-hydroxy-N-[[3-[5-hydroxy-4-(1H-pyrrolo[3,2-c]pyridin-2-yl)pyrazol-1-yl]phenyl]methyl]propanamide


Mass: 377.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H19N5O3
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 376 / 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

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: 1.0008 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0008 Å / Relative weight: 1
ReflectionResolution: 1.45→47.63 Å / Num. obs: 94781 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 8.34 % / Biso Wilson estimate: 28.036 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.072 / Χ2: 1.133 / Net I/σ(I): 15.32 / Num. measured all: 790132
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.491.3631.5258074691769170.6671.45100
1.49-1.531.1071.956605680168010.7511.179100
1.53-1.570.8312.5653289657365730.830.886100
1.57-1.620.6113.5354060646264620.9040.651100
1.62-1.670.4394.9655183621962190.9440.466100
1.67-1.730.3396.4453376603160280.9650.359100
1.73-1.80.2548.5750393582058190.9780.269100
1.8-1.870.19511.0647362561656130.9850.20799.9
1.87-1.960.14614.4345680538253740.9910.15599.9
1.96-2.050.11818.1345152516251540.9940.12699.8
2.05-2.160.09521.7441779490648910.9960.199.7
2.16-2.290.08223.8237189468046510.9960.08899.4
2.29-2.450.0726.7434740440243620.9970.07599.1
2.45-2.650.06330.0233442410540610.9970.06798.9
2.65-2.90.05532.7630453378537460.9980.05899
2.9-3.240.0534.0725355345733960.9980.05398.2
3.24-3.740.04637.0522113306530020.9980.04997.9
3.74-4.590.04240.820794262525430.9980.04596.9
4.59-6.480.03939.8615689207420000.9990.04196.4
6.48-47.630.03440.819404123011690.9990.03795

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.4.0077refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: inhouse model

Resolution: 1.45→47.62 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.881 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.049 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: the numbering follows that of the unprocessed precursor Gln426 not defined by electron density chiral centre of ligand unambiguously assigned to (S) despite bad electron density. HYDROGENS ...Details: the numbering follows that of the unprocessed precursor Gln426 not defined by electron density chiral centre of ligand unambiguously assigned to (S) despite bad electron density. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1875 4747 5 %RANDOM
Rwork0.1786 ---
obs0.179 89893 99.3 %-
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: 65.05 Å2 / Biso mean: 19.383 Å2 / Biso min: 11.63 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.64 Å2
Refinement stepCycle: final / Resolution: 1.45→47.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2342 0 66 376 2784
Biso mean--36.85 36.56 -
Num. residues----303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212533
X-RAY DIFFRACTIONr_bond_other_d0.0020.021694
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.983467
X-RAY DIFFRACTIONr_angle_other_deg2.6463.0074108
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9665321
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.12722.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3315404
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5591519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212798
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02504
X-RAY DIFFRACTIONr_mcbond_it0.9761.51534
X-RAY DIFFRACTIONr_mcbond_other0.2241.5630
X-RAY DIFFRACTIONr_mcangle_it1.77522488
X-RAY DIFFRACTIONr_scbond_it2.5733999
X-RAY DIFFRACTIONr_scangle_it4.1394.5969
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 329 -
Rwork0.286 6561 -
all-6890 -
obs--99.67 %

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