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- PDB-3bf6: Thrombin:suramin complex -

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Basic information

Entry
Database: PDB / ID: 3bf6
TitleThrombin:suramin complex
Components
  • PHE-PRO-ARG
  • Thrombin, HEAVY CHAIN
  • Thrombin, LIGHT CHAIN
KeywordsHYDROLASE / Thrombin / suramin / blood / coagulation / Acute phase / Blood coagulation / Cleavage on pair of basic residues / Disease mutation / Gamma-carboxyglutamic acid / Glycoprotein / Kringle / Protease / Secreted / Serine protease / Zymogen
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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / 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 / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / 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 / Regulation of Complement cascade / acute-phase response / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / positive regulation of insulin secretion / platelet activation / response to wounding / Golgi lumen / positive regulation of protein localization to nucleus / 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 / 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 / blood microparticle / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / 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. / Kringle domain profile. ...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-SVR / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsLima, L.M.T.R. / Polikarpov, I. / Monteiro, R.Q.
Citation
Journal: Biochim.Biophys.Acta / Year: 2009
Title: Structural and thermodynamic analysis of thrombin:suramin interaction in solution and crystal phases.
Authors: Lima, L.M. / Becker, C.F. / Giesel, G.M. / Marques, A.F. / Cargnelutti, M.T. / de Oliveira Neto, M. / Queiroz Monteiro, R. / Verli, H. / Polikarpov, I.
#1: Journal: INT.J.BIOCHEM.CELL BIOL. / Year: 2004
Title: Suramin interaction with human alpha-thrombin: inhibitory effects and binding studies
Authors: Monteiro, R.Q. / Campana, P.T. / Melo, P.A. / Bianconi, M.L.
#2: Journal: Toxicon / Year: 2007
Title: Suramin counteracts the haemostatic disturbances produced by Bothrops jararaca snake venom.
Authors: Fernandes, R.S. / Assafim, M. / Arruda, E.Z. / Melo, P.A. / Zingali, R.B. / Monteiro, R.Q.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 15, 2015Group: Structure summary

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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
I: PHE-PRO-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5944
Polymers34,2963
Non-polymers1,2971
Water4,089227
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.381, 73.471, 114.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide Thrombin, LIGHT CHAIN /


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 328-363 / Source method: isolated from a natural source / Details: human plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein Thrombin, HEAVY CHAIN /


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 364-622 / Source method: isolated from a natural source / Details: human plasma / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide PHE-PRO-ARG


Mass: 419.498 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic Peptide
#4: Chemical ChemComp-SVR / 8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFONIC ACID / SURAMIN / Suramin


Mass: 1297.280 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C51H40N6O23S6 / Comment: medication*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, 25% v/v t-butanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→61.898 Å / Num. all: 13134 / Num. obs: 12905 / % possible obs: 95.3 % / Observed criterion σ(I): 3.5 / Redundancy: 7.6 % / Biso Wilson estimate: 28.73 Å2 / Rmerge(I) obs: 0.191 / Rsym value: 0.191 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.647.10.5971.31274118050.59793.7
2.64-2.87.20.4721.61250217470.47294.9
2.8-2.997.10.3692.11172216410.36996.3
2.99-3.237.30.25531156215900.25598.4
3.23-3.547.70.1644.71137014770.16499
3.54-3.958.20.1495.1881710810.14979
3.95-4.568.30.0987.71004612080.09899.2
4.56-5.598.50.1067.1881110410.10699.4
5.59-7.918.30.1465.268028190.14699.8
7.91-35.097.50.0887.737284960.08898.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345dtbdata collection
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→34.99 Å / Cor.coef. Fo:Fc: 0.881 / Cor.coef. Fo:Fc free: 0.823 / SU B: 10.369 / SU ML: 0.234 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.769 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.282 645 5 %RANDOM
Rwork0.228 ---
obs0.231 12843 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.927 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2---0.09 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.5→34.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2282 0 86 227 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222502
X-RAY DIFFRACTIONr_angle_refined_deg1.0512.0053406
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1715291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.20323.13115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83415434
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.8881522
X-RAY DIFFRACTIONr_chiral_restr0.0660.2343
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021933
X-RAY DIFFRACTIONr_nbd_refined0.170.21276
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0880.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1180.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.218
X-RAY DIFFRACTIONr_mcbond_it0.1611.51490
X-RAY DIFFRACTIONr_mcangle_it0.29322330
X-RAY DIFFRACTIONr_scbond_it0.29731250
X-RAY DIFFRACTIONr_scangle_it0.4934.51076
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 47 -
Rwork0.275 870 -
all-917 -
obs--94.44 %

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