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- PDB-5mjt: Thrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-... -

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Basic information

Entry
Database: PDB / ID: 5mjt
TitleThrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-diphenylpropanoyl) -N- (3-chlorobenzyl) pyrrolidine-2-carboxamide
Components
  • Hirudin variant-2
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsHYDROLASE / COAGULATION / BLOOD CLOTTING / CONVERTION OF FIBRINOGEN TO FIBRIN / BLOOD CLOTTING INHIBITOR / PREORGANIZATION / GLYCOSILATION / BLOOD
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / regulation of cytosolic calcium ion concentration / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / 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 / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / blood microparticle / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / 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 / 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
Chem-23U / PHOSPHATE ION / Prothrombin / Hirudin variant-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMarca, A. / Sandner, A. / Heine, A. / Klebe, G.
CitationJournal: to be published
Title: Thrombin Mutant A190S in complex with (S) -1 - ((R) -2-amino-3,3-diphenylpropanoyl) -N- (3-chlorobenzyl) pyrrolidine-2-carboxamide
Authors: Marca, A. / Ngo, K. / Sandner, A. / Heine, A. / Klebe, G.
History
DepositionDec 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
D: Hirudin variant-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,58313
Polymers35,4413
Non-polymers1,14210
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-40 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.492, 71.613, 72.129
Angle α, β, γ (deg.)90.00, 99.73, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-424-

HOH

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Components

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Protein/peptide , 2 types, 2 molecules LD

#1: Protein/peptide Thrombin light chain / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F2 / Plasmid: PT2 A190S / Details (production host): pET 21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirudin variant-2


Mass: 1548.580 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: http://shop.bachem.com/h-7525.html contains sulfated tyrosine
Source: (synth.) Hirudo medicinalis (medicinal leech) / References: UniProt: P09945

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Protein , 1 types, 1 molecules H

#2: Protein Thrombin heavy chain / Coagulation factor II


Mass: 29796.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Alanine 190 mutated to Serine. / Source: (gene. exp.) Homo sapiens (human) / Tissue: Blood / Gene: F2 / Plasmid: PT2 A190S / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: P00734, thrombin

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Non-polymers , 6 types, 225 molecules

#4: Chemical ChemComp-23U / beta-phenyl-D-phenylalanyl-N-(3-chlorobenzyl)-L-prolinamide


Mass: 461.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H28ClN3O2
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20 mM Sodium dihydrogen phosphate ph 7.5, 350 mM NaCl, 27% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 26, 2016 / Details: Sagitally bended Si111-crystal
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→49.498 Å / Num. obs: 64401 / % possible obs: 93.6 % / Redundancy: 4 % / CC1/2: 0.999 / Rsym value: 0.052 / Net I/σ(I): 16
Reflection shellResolution: 1.4→1.48 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / CC1/2: 0.84 / % possible all: 91.6

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
CootPunta Carretas 0.8-premodel building
XDSdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→49.498 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.49
RfactorNum. reflection% reflection
Rfree0.1722 3220 5 %
Rwork0.1479 --
obs0.1491 64399 93.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→49.498 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 74 215 2621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112503
X-RAY DIFFRACTIONf_angle_d1.2473385
X-RAY DIFFRACTIONf_dihedral_angle_d19.517967
X-RAY DIFFRACTIONf_chiral_restr0.093349
X-RAY DIFFRACTIONf_plane_restr0.008454
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3981-1.4190.24941280.25292437X-RAY DIFFRACTION87
1.419-1.44120.25321390.23972645X-RAY DIFFRACTION93
1.4412-1.46480.25151410.22072676X-RAY DIFFRACTION93
1.4648-1.490.22671370.20492614X-RAY DIFFRACTION93
1.49-1.51710.22521370.2022596X-RAY DIFFRACTION91
1.5171-1.54630.20921300.17922464X-RAY DIFFRACTION87
1.5463-1.57790.22881400.16312675X-RAY DIFFRACTION95
1.5779-1.61220.17341440.15722734X-RAY DIFFRACTION95
1.6122-1.64970.17231410.15182670X-RAY DIFFRACTION95
1.6497-1.6910.17771410.1472689X-RAY DIFFRACTION95
1.691-1.73670.15961420.14582696X-RAY DIFFRACTION95
1.7367-1.78780.17621430.13652702X-RAY DIFFRACTION95
1.7878-1.84550.14051400.13072671X-RAY DIFFRACTION94
1.8455-1.91150.15361350.13192565X-RAY DIFFRACTION91
1.9115-1.9880.14341370.12662598X-RAY DIFFRACTION91
1.988-2.07850.15111440.12662748X-RAY DIFFRACTION97
2.0785-2.1880.15521440.1252724X-RAY DIFFRACTION97
2.188-2.32510.16781440.13242746X-RAY DIFFRACTION96
2.3251-2.50470.16191440.13382721X-RAY DIFFRACTION95
2.5047-2.75670.17251360.14682586X-RAY DIFFRACTION90
2.7567-3.15550.16411440.14872738X-RAY DIFFRACTION96
3.1555-3.97540.17291450.14412761X-RAY DIFFRACTION97
3.9754-49.5290.1721440.15312723X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0109-0.01630.00630.0213-0.00830.02050.02320.0594-0.0124-0.1538-0.1028-0.093-0.2292-0.0655-0.0030.1370.0429-0.00090.11390.0040.13285.416516.732918.1258
20.0570.0280.02850.0651-0.01350.03530.0569-0.0015-0.0148-0.0674-0.1308-0.0014-0.1107-0.1162-0.00190.1290.0604-0.00180.1456-0.01570.1494-3.29514.06520.7244
30.0221-0.0174-0.0110.0371-0.02060.0314-0.0263-0.13730.19460.20220.0116-0.0938-0.1812-0.0628-0.00070.15890.03120.01910.1478-0.01360.16710.14499.363734.4858
40.0405-0.01980.01970.0074-0.00790.00640.17570.0625-0.108-0.0564-0.16140.11370.0058-0.01760.00030.11960.0264-0.02360.1331-0.01870.15331.19912.450717.3052
50.34610.0172-0.01770.39550.02180.04280.230.39120.0229-0.2671-0.2823-0.0750.11480.2359-0.12240.20480.12610.00690.237-0.01330.109415.46311.03478.4477
60.18520.00640.22620.26720.08730.47750.21010.28180.0429-0.1689-0.1302-0.04740.13690.12950.11750.14840.09940.00460.1979-0.00590.126923.3995-5.001514.1653
70.07930.0437-0.04870.49170.00740.36730.1210.3452-0.0904-0.4365-0.18280.07670.27420.2062-0.31710.25560.1578-0.01040.2863-0.04140.07369.06032.30273.4825
80.35460.33570.10150.62750.37670.37990.18720.26650.0070.0764-0.1255-0.2525-0.02210.11720.14650.10290.08380.05290.20770.02690.117126.064-1.327218.1634
90.561-0.49320.04970.4530.03030.11410.03610.07730.1112-0.0163-0.0853-0.0803-0.02310.0493-0.03010.11190.01890.00680.11620.01180.116812.44439.78521.7986
100.2036-0.05950.06350.1028-0.03240.10670.16330.031-0.216-0.0210.0080.18160.223-0.03270.01760.1640.0357-0.05110.1217-0.0370.16964.3127-5.600320.2352
110.01110.0255-0.03280.0267-0.03020.0287-0.0458-0.0392-0.02830.19840.0549-0.04880.03510.08840.00250.15960.0264-0.00530.1120.00750.136218.9281-8.615335.724
120.1302-0.15840.05840.1804-0.10630.07530.0983-0.0041-0.1613-0.0155-0.02270.06720.17130.0650.00380.1440.0082-0.00620.10520.00810.1567.0076-6.848227.8432
130.3716-0.16740.06760.0837-0.0850.3270.0483-0.0171-0.0531-0.0264-0.0420.03850.01390.02370.01730.10120.02340.00560.0840.00030.111110.6190.975927.366
140.04450.08790.03690.20790.08180.03550.04360.07140.3301-0.0036-0.0592-0.2543-0.10860.18040.00330.1151-0.01910.04150.15390.05250.256526.53510.419122.6757
150.0232-0.02860.01310.0539-0.01710.00990.11620.29710.0568-0.2205-0.0647-0.0198-0.0784-0.00120.03780.48630.23090.03120.5385-0.10460.094411.97560.7352-3.2164
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1C through 7 )
2X-RAY DIFFRACTION2chain 'L' and (resid 8 through 14B )
3X-RAY DIFFRACTION3chain 'L' and (resid 14C through 17 )
4X-RAY DIFFRACTION4chain 'H' and (resid 16 through 29 )
5X-RAY DIFFRACTION5chain 'H' and (resid 30 through 50 )
6X-RAY DIFFRACTION6chain 'H' and (resid 51 through 60 )
7X-RAY DIFFRACTION7chain 'H' and (resid 61 through 80 )
8X-RAY DIFFRACTION8chain 'H' and (resid 81 through 103 )
9X-RAY DIFFRACTION9chain 'H' and (resid 104 through 140 )
10X-RAY DIFFRACTION10chain 'H' and (resid 141 through 164 )
11X-RAY DIFFRACTION11chain 'H' and (resid 165 through 179 )
12X-RAY DIFFRACTION12chain 'H' and (resid 180 through 197 )
13X-RAY DIFFRACTION13chain 'H' and (resid 198 through 231 )
14X-RAY DIFFRACTION14chain 'H' and (resid 232 through 245 )
15X-RAY DIFFRACTION15chain 'D' and (resid 518 through 528 )

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