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- PDB-1w8b: Factor7 - 413 complex -

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Basic information

Entry
Database: PDB / ID: 1w8b
TitleFactor7 - 413 complex
Components(BLOOD COAGULATION FACTOR VIIA) x 2
KeywordsHYDROLASE / SERINE PROTEASE / COAGULATION / ENZYME COMPLEX
Function / homology
Function and homology information


coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / response to genistein / serine-type peptidase complex / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway ...coagulation factor VIIa / response to Thyroid stimulating hormone / response to astaxanthin / response to thyrotropin-releasing hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to carbon dioxide / response to genistein / serine-type peptidase complex / response to vitamin K / positive regulation of platelet-derived growth factor receptor signaling pathway / positive regulation of leukocyte chemotaxis / response to thyroxine / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of blood coagulation / animal organ regeneration / positive regulation of TOR signaling / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian expression / circadian rhythm / protein processing / Golgi lumen / response to estrogen / blood coagulation / response to estradiol / : / 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 / 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 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / 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-413 / Coagulation factor VII
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsAckermann, J. / Alig, L. / Banner, D.W. / Boehm, H.-J. / Groebke-Zbinden, K. / Hilpert, K. / Lave, T. / Kuehne, H. / Obst-Sander, U. / Riederer, M.A. ...Ackermann, J. / Alig, L. / Banner, D.W. / Boehm, H.-J. / Groebke-Zbinden, K. / Hilpert, K. / Lave, T. / Kuehne, H. / Obst-Sander, U. / Riederer, M.A. / Stahl, M. / Tschopp, T.B. / Weber, L. / Wessel, H.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Selective and Orally Bioavailable Phenylglycine Tissue Factor/Factor Viia Inhibitors
Authors: Groebke-Zbinden, K. / Obst-Sander, U. / Hilpert, K. / Kuehne, H. / Banner, D.W. / Boehm, H.-J. / Stahl, M. / Ackermann, J. / Alig, L. / Weber, L. / Wessel, H.P. / Riederer, M.A. / Tschopp, T.B. / Lave, T.
History
DepositionSep 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 25, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4Nov 6, 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
H: BLOOD COAGULATION FACTOR VIIA
L: BLOOD COAGULATION FACTOR VIIA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9544
Polymers34,3752
Non-polymers5792
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.846, 82.846, 147.768
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein BLOOD COAGULATION FACTOR VIIA / SERUM PROTHROMBIN CONVERSION ACCELERATOR / SPCA / PROCONVERTIN / EPTACOG ALFA / NOVOSEVEN


Mass: 28103.256 Da / Num. of mol.: 1 / Fragment: FACTOR VII HEAVY CHAIN, RESIDUES 213-466
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa
#2: Protein BLOOD COAGULATION FACTOR VIIA / SERUM PROTHROMBIN CONVERSION ACCELERATOR / SPCA / PROCONVERTIN / EPTACOG ALFA / NOVOSEVEN


Mass: 6272.113 Da / Num. of mol.: 1 / Fragment: FACTOR VII LIGHT CHAIN, RESIDUES 148-204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P08709, coagulation factor VIIa
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-413 / (S)-[(R)-2-(4-BENZYLOXY-3-METHOXY-PHENYL)-2-(4-CARBAMIMIDOYL-PHENYLAMINO)-ACETYLAMINO]-PHENYL-ACETIC ACID


Mass: 538.594 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H30N4O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
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: 3.6 Å3/Da / Density % sol: 65 %
Description: ONLY 27DEGREES OF DATA WERE COLLECTED, SO COMPLETENESS IS VERY POOR. ALSO THERE WAS SEVERE ICING.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 24, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.82→20 Å / Num. obs: 23089 / % possible obs: 75 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.3
Reflection shellResolution: 2.82→2.92 Å / % possible all: 62

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0Y

1w0y


Resolution: 3→72.36 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.843 / SU B: 14.796 / SU ML: 0.278 / Cross valid method: THROUGHOUT / ESU R Free: 0.503 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENZYME-INHIBITOR COMPLEX WAS RECENTLY REDETERMINED AT HIGH RESOLUTION IN A DIFFERENT SPACE GROUP (1W7X.PDB). THIS ORIGINAL STRUCTURE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENZYME-INHIBITOR COMPLEX WAS RECENTLY REDETERMINED AT HIGH RESOLUTION IN A DIFFERENT SPACE GROUP (1W7X.PDB). THIS ORIGINAL STRUCTURE IS AT LOW RESOLUTION AND THE DATA IS INCOMPLETE. NEVERTHELESS THE INHIBITOR BIND MODE IS WELL DETERMINED. CURIOUSLY ONE INHIBITOR SUBSTITUENT IN THIS STRUCTURE IS DISPLACED FROM ITS POSITION SEEN IN RELATED STRUCTURES, AND RESIDUES FROM THE NEXT MOLECULE IN THE CRYSTAL FILL THE BINDING POCKET. THE LOOP 140-150 IS NOT SEEN, AND POSSIBLY SUFFERED PROTEOLYSIS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 392 4.8 %RANDOM
Rwork0.194 ---
obs0.197 7847 75.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.41 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 3→72.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2334 0 41 59 2434
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212419
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1361.9713297
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7185299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.11423.09397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88115371
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.311516
X-RAY DIFFRACTIONr_chiral_restr0.0780.2363
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21111
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21608
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2127
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.234
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3941.51530
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.69822412
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.69831035
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.234.5885
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.4 36
Rwork0.234 603

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