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- PDB-3po1: Thrombin in complex with Benzothiazole Guanidine -

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Basic information

Entry
Database: PDB / ID: 3po1
TitleThrombin in complex with Benzothiazole Guanidine
Components
  • (Thrombin heavy ...) x 2
  • Thrombin light chain
  • thrombin peptide
KeywordsHYDROLASE/HYDROLASE inhibitor / serine protease / coagulation factor II / HYDROLASE-HYDROLASE inhibitor complex
Function / homology
Function and homology information


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle 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. / Kringle-like fold / 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
ACETATE ION / Chem-MKY / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsXue, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Discovery of benzothiazole guanidines as novel inhibitors of thrombin and trypsin IV.
Authors: Karle, M. / Knecht, W. / Xue, Y.
History
DepositionNov 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
B: Thrombin heavy chain
C: Thrombin heavy chain
D: thrombin peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5637
Polymers33,1874
Non-polymers3763
Water2,522140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10540 Å2
ΔGint-70 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.662, 71.414, 71.880
Angle α, β, γ (deg.)90.000, 99.820, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 2 types, 2 molecules AD

#1: Protein/peptide Thrombin light chain


Mass: 3188.627 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#4: Protein/peptide thrombin peptide


Mass: 1291.337 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human)

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Thrombin heavy ... , 2 types, 2 molecules BC

#2: Protein Thrombin heavy chain


Mass: 17070.738 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein Thrombin heavy chain


Mass: 11636.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin

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Non-polymers , 4 types, 143 molecules

#5: Chemical ChemComp-MKY / ethyl [(2Z)-2-(carbamimidoylimino)-6-hydroxy-1,3-benzothiazol-3(2H)-yl]acetate


Mass: 294.330 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H14N4O3S
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7.3
Details: 0.05 M sodium phosphate, 28% PEG8000, pH 7.3, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→70.89 Å / Num. all: 39772 / Num. obs: 39772 / % possible obs: 96.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.3 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 13.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.65-1.693.30.342.2925528420.3495.3
1.69-1.743.30.2932.6917328090.29395.4
1.74-1.793.30.2143.5903427580.21495.8
1.79-1.843.30.1734.3887027000.17395.8
1.84-1.913.30.1415.2851625990.14196.4
1.91-1.973.30.1056.8825225130.10596.3
1.97-2.053.30.0847.9801324390.08496.7
2.05-2.133.30.0749.2769723400.07496.9
2.13-2.223.30.0669.7747622750.06697
2.22-2.333.30.0619.8710221590.06197.2
2.33-2.463.30.0599.5685020860.05997.4
2.46-2.613.30.0599.7640019570.05997.7
2.61-2.793.30.0599595818320.05997.9
2.79-3.013.30.0579.8566517320.05798
3.01-3.33.30.0569532316260.05698.3
3.3-3.693.20.0549.8460614190.05498.4
3.69-4.263.20.0511.1414412880.0598.8
4.26-5.223.20.04114.2354410970.04198.8
5.22-7.383.20.04313.927158510.04398.9
7.38-27.1762.90.04113.912974500.04192.6

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.5data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→27.176 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.2878 / WRfactor Rwork: 0.2526 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7908 / SU B: 2.652 / SU ML: 0.089 / SU R Cruickshank DPI: 0.1192 / SU Rfree: 0.1166 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 1904 4.9 %RANDOM
Rwork0.2271 ---
all0.2287 39772 --
obs0.2287 38491 93.51 %-
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: 55.38 Å2 / Biso mean: 28.5089 Å2 / Biso min: 13.45 Å2
Baniso -1Baniso -2Baniso -3
1-2.65 Å20 Å20.38 Å2
2---1.35 Å20 Å2
3----1.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.117 Å0.119 Å
Refinement stepCycle: LAST / Resolution: 1.65→27.176 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 25 140 2492
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222410
X-RAY DIFFRACTIONr_angle_refined_deg1.3671.9833256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0045282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.68723.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5641520
X-RAY DIFFRACTIONr_chiral_restr0.0970.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021842
X-RAY DIFFRACTIONr_nbd_refined0.2070.21069
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.2172
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2730.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2190.28
X-RAY DIFFRACTIONr_mcbond_it0.841.51425
X-RAY DIFFRACTIONr_mcangle_it1.47722296
X-RAY DIFFRACTIONr_scbond_it1.95431039
X-RAY DIFFRACTIONr_scangle_it3.0424.5960
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 126 -
Rwork0.302 2396 -
all-2522 -
obs--84.38 %

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