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- PDB-1uvs: BOVINE THROMBIN--BM51.1011 COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1uvs
TitleBOVINE THROMBIN--BM51.1011 COMPLEX
Components(THROMBIN) x 2
KeywordsSERINE PROTEASE / HYDROLASE / THROMBIN / BLOOD COAGULATION
Function / homology
Function and homology information


positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) ...positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / neutrophil-mediated killing of gram-negative bacterium / cytolysis by host of symbiont cells / thrombin / regulation of blood coagulation / 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 / negative regulation of blood coagulation / blood coagulation, common pathway / 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 / regulation of cytosolic calcium ion concentration / Peptide ligand-binding receptors / positive regulation of receptor signaling pathway via JAK-STAT / fibrinolysis / positive regulation of release of sequestered calcium ion into cytosol / Intrinsic Pathway of Fibrin Clot Formation / zymogen activation / Thrombin signalling through proteinase activated receptors (PARs) / Regulation of Complement cascade / lipopolysaccharide binding / acute-phase response / Cell surface interactions at the vascular wall / serine-type endopeptidase complex / negative regulation of proteolysis / growth factor activity / positive regulation of protein localization to nucleus / response to wounding / platelet activation / Golgi lumen / positive regulation of reactive oxygen species metabolic process / G alpha (q) signalling events / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / positive regulation of phosphatidylinositol 3-kinase signaling / heparin binding / regulation of cell shape / positive regulation of cell growth / collagen-containing extracellular matrix / blood microparticle / antimicrobial humoral immune response mediated by antimicrobial peptide / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / signaling receptor binding / proteolysis / serine-type endopeptidase activity / endoplasmic reticulum lumen / calcium ion binding / positive regulation of cell population proliferation / extracellular space / extracellular exosome / extracellular region / membrane / plasma membrane
Similarity search - Function
Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Thrombin light chain / Kringle domain / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain profile. ...Prothrombin/thrombin / Thrombin light chain domain superfamily / Thrombin light chain / Thrombin light chain / Kringle domain / Kringle superfamily / Kringle, conserved site / Kringle domain signature. / Kringle / Kringle domain profile. / Kringle domain / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / 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. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / 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-I11 / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsEngh, R.A. / Huber, R.
CitationJournal: Structure / Year: 1996
Title: Enzyme flexibility, solvent and 'weak' interactions characterize thrombin-ligand interactions: implications for drug design.
Authors: Engh, R.A. / Brandstetter, H. / Sucher, G. / Eichinger, A. / Baumann, U. / Bode, W. / Huber, R. / Poll, T. / Rudolph, R. / von der Saal, W.
History
DepositionOct 16, 1996Processing site: BNL
Revision 1.0Nov 19, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: THROMBIN
H: THROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3433
Polymers33,8772
Non-polymers4671
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-18 kcal/mol
Surface area11710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.684, 81.684, 186.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein/peptide THROMBIN / / FACTOR II


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
#2: Protein THROMBIN / / FACTOR II


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P00734, thrombin
#3: Chemical ChemComp-I11 / [[CYCLOHEXANESULFONYL-GLYCYL]-3[PYRIDIN-4-YL-AMINOMETHYL]ALANYL]PIPERIDINE


Mass: 466.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H36N5O4S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.65 Å3/Da / Density % sol: 53.56 %
Crystal grow
*PLUS
pH: 6.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlthrombin1drop
225 mMcitrate1drop
31 mMEDTA1drop
410 mMDMSO1drop
50.2 Mlithium sulfate1drop
60.1 MTris1drop
730 %PEG40001drop
80.2 Mlithium sulfate1reservoir
90.1 MTris1reservoir
1030 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→22 Å / Num. obs: 7921 / Rmerge(I) obs: 0.079

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Processing

Software
NameClassification
SAINTdata scaling
PROTEINdata reduction
X-PLORmodel building
X-PLORrefinement
SAINTdata reduction
PROTEINdata scaling
X-PLORphasing
RefinementResolution: 2.8→8 Å / Cross valid method: FREE R / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.28 -10 %
Rwork0.208 --
obs0.208 6873 74.7 %
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2108 0 32 38 2178
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.09
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.95
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.8→8 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.387 48 -
Rwork0.256 345 -
obs--35 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.95

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