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- PDB-1jbu: Coagulation Factor VII Zymogen (EGF2/Protease) in Complex with In... -

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Basic information

Entry
Database: PDB / ID: 1jbu
TitleCoagulation Factor VII Zymogen (EGF2/Protease) in Complex with Inhibitory Exosite Peptide A-183
Components
  • (COAGULATION FACTOR ...Coagulation) x 2
  • Peptide exosite inhibitor A-183
KeywordsHYDROLASE/HYDROLASE INHIBITOR / shifted registration / beta-strands / 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 / 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. / Serine proteases, trypsin family, serine active site. / 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
BENZAMIDINE / Coagulation factor VII
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEigenbrot, C. / Kirchhofer, D. / Dennis, M.S. / Santell, L. / Lazarus, R.A. / Stamos, J. / Ultsch, M.H.
Citation
Journal: Structure / Year: 2001
Title: The factor VII zymogen structure reveals reregistration of beta strands during activation.
Authors: Eigenbrot, C. / Kirchhofer, D. / Dennis, M.S. / Santell, L. / Lazarus, R.A. / Stamos, J. / Ultsch, M.H.
#1: Journal: To be Published
Title: A Novel Exosite on Coagulation Factor VIIa and its Molecular Interactions with a New Class of Peptide Inhibitors
Authors: Roberge, M. / Santell, L. / Dennis, M.S. / Eigenbrot, C. / Dwyer, M.A. / Lazarus, R.A.
#2: Journal: Nature / Year: 1996
Title: The Crystal Structure of the Complex of Blood Coagulation Factor VIIa with Soluble Tissue Factor
Authors: Banner, D.W. / D'Arcy, A. / Chene, C. / Winkler, F.K. / Guha, A. / Konigsberg, W.H. / Nemerson, Y. / Kirchhofer, D.
#3: Journal: J.Mol.Biol. / Year: 1999
Title: Structure of Extracellular Tissue Factor Complexed with Factor VIIa Inhibited with a BPTI Mutant
Authors: Zhang, E. / St.Charles, R. / Tulinsky, A.
#4: Journal: J.STRUCT.BIOL. / Year: 1999
Title: Crystal Structure of Active Site-inhibited Human Coagulation Factor VIIa (des-Gla)
Authors: Kemball-Cook, G. / Johnson, D.J. / Tuddenham, E.G. / Harlos, K.
#5: Journal: Proc.Natl.Acad.Sci.USA / Year: 1999
Title: Structure of Human Factor VIIa and its Implications for the Triggering of Blood Coagulation
Authors: Pike, A.C. / Brzozowski, A.M. / Roberts, S.M. / Olsen, O.H. / Persson, E.
#6: Journal: Nature / Year: 2000
Title: Peptide Exosite Inhibitors of Factor VIIa as Anticoagulants
Authors: Dennis, M.S. / Eigenbrot, C. / Skelton, N.J. / Ultsch, M.H. / Santell, L. / Dwyer, M.A. / O'Connell, M.P. / Lazarus, R.A.
History
DepositionJun 6, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Jan 24, 2018Group: Advisory / Database references
Category: citation_author / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation_author.name
Revision 1.4Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The authors are uncertain of the true identity of the het group BEN, and used benzamidine ...HETEROGEN The authors are uncertain of the true identity of the het group BEN, and used benzamidine as a convenience.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: COAGULATION FACTOR VII
L: COAGULATION FACTOR VII
X: Peptide exosite inhibitor A-183
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1915
Polymers36,9753
Non-polymers2162
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-30 kcal/mol
Surface area14640 Å2
MethodPISA
2
L: COAGULATION FACTOR VII

H: COAGULATION FACTOR VII
X: Peptide exosite inhibitor A-183
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1915
Polymers36,9753
Non-polymers2162
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-30 kcal/mol
Surface area15140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.440, 84.510, 84.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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COAGULATION FACTOR ... , 2 types, 2 molecules HL

#1: Protein COAGULATION FACTOR VII / SERUM PROTHROMBIN CONVERSION ACCELERATOR


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: Heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcGP67 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five / References: UniProt: P08709, coagulation factor VIIa
#2: Protein COAGULATION FACTOR VII / SERUM PROTHROMBIN CONVERSION ACCELERATOR


Mass: 6871.753 Da / Num. of mol.: 1 / Fragment: Light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pAcGP67 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): High-Five / References: UniProt: P08709, coagulation factor VIIa

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Protein/peptide , 1 types, 1 molecules X

#3: Protein/peptide Peptide exosite inhibitor A-183


Mass: 2000.189 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: synthetic construct / Plasmid: pA-100-Z / Production host: Escherichia coli (E. coli) / Strain (production host): 27C7

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Non-polymers , 3 types, 200 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, ammonium sulfate, glycerol, PEG 400, benzamidine, calcium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMHEPES1drop
2850 mMammonium sulfate1drop
37.5 %glycerol1drop
40.85 %PEG4001drop
55 mg/mlrF71drop
65 mMbenzamidine1drop
75 mM1dropCa2+
80.3 mg/mlA-1831drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.05 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 8, 1999
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2→35 Å / Num. all: 33624 / Num. obs: 33624 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.044 % / Biso Wilson estimate: 33.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.77 % / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3318 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 135991
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 3318 / Num. measured obs: 12516

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SCALEPACKdata scaling
AMoREphasing
X-PLOR98.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1DAN

1dan


Resolution: 2→35 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.227 698 2.1 %RANDOM
Rwork0.204 ---
all0.212 33404 --
obs0.212 33404 99.9 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.01 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 14 198 2627
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d24.2
X-RAY DIFFRACTIONx_improper_angle_d1.1
X-RAY DIFFRACTIONx_mcbond_it2.973
X-RAY DIFFRACTIONx_mcangle_it4.474
X-RAY DIFFRACTIONx_scbond_it4.074
X-RAY DIFFRACTIONx_scangle_it5.96
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.34 59 1.8 %
Rwork0.313 3230 -
obs-3259 99.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_XPLOR_PARHCSDXMSI_XPLOR_TOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM.SO4TOP.SO4
X-RAY DIFFRACTION3PARWAT.PROTOPWAT.PRO
X-RAY DIFFRACTION4PARAM.BDNTOP.BDN
Software
*PLUS
Name: X-PLOR(ONLINE) / Version: 98.1 / Classification: refinement
Refinement
*PLUS
σ(F): 0.2 / % reflection Rfree: 2.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.1
X-RAY DIFFRACTIONx_mcbond_it3
X-RAY DIFFRACTIONx_scbond_it4
X-RAY DIFFRACTIONx_mcangle_it4
X-RAY DIFFRACTIONx_scangle_it6
LS refinement shell
*PLUS
Rfactor Rfree: 0.34 / % reflection Rfree: 1.8 % / Rfactor Rwork: 0.313 / Rfactor obs: 0.318

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