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- PDB-9c50: Replacement of a single residue changes the primary specificity o... -

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Basic information

Entry
Database: PDB / ID: 9c50
TitleReplacement of a single residue changes the primary specificity of thrombin
Components
  • FPF
  • Thrombin A-chain
  • Thrombin B-chain
KeywordsBLOOD CLOTTING / coagulation / Thrombin
Function / homology
Function and homology information


cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway ...cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin-activated receptor signaling pathway / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / Defective F8 cleavage by thrombin / ligand-gated ion channel signaling pathway / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / 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 / negative regulation of proteolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of cytokine production involved in inflammatory response / positive regulation of release of sequestered calcium ion into cytosol / Peptide ligand-binding receptors / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / lipopolysaccharide binding / growth factor activity / positive regulation of insulin secretion / platelet activation / positive regulation of protein localization to nucleus / response to wounding / 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 / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cell growth / : / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDei Rossi, A. / Deavila, S. / Mohammed, B.M. / Korolev, S. / Di Cera, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL049413 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL139554 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL147821 United States
CitationJournal: J.Thromb.Haemost. / Year: 2025
Title: Replacement of a single residue changes the primary specificity of thrombin.
Authors: Dei Rossi, A. / Deavila, S. / Mohammed, B.M. / Korolev, S. / Di Cera, E.
History
DepositionJun 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin A-chain
B: Thrombin B-chain
C: Thrombin A-chain
D: Thrombin B-chain
E: FPF
F: FPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9738
Polymers71,9276
Non-polymers462
Water2,180121
1
A: Thrombin A-chain
B: Thrombin B-chain
E: FPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9874
Polymers35,9643
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Thrombin A-chain
D: Thrombin B-chain
F: FPF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9874
Polymers35,9643
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.150, 76.732, 89.588
Angle α, β, γ (deg.)90.00, 113.77, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein/peptide Thrombin A-chain / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734
#2: Protein Thrombin B-chain


Mass: 31425.033 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Thrombin B-Chain + C-terminus HPC4 tag (YLEDQVDPRLIDGK)
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Cell line (production host): BHK / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734
#3: Protein/peptide FPF


Mass: 441.950 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.9 Å3/Da / Density % sol: 57.64 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1 M succinic acid, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 14, 2024
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 27672 / % possible obs: 96.4 % / Redundancy: 2.7 % / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.068 / Rrim(I) all: 0.122 / Χ2: 0.9 / Net I/σ(I): 6.8 / Num. measured all: 75189
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.49-2.532.70.67713660.7130.9120.4620.8220.79395.6
2.53-2.582.70.58613370.7650.9310.4010.7130.78294.3
2.58-2.632.70.58313770.7750.9350.3970.7080.80195.6
2.63-2.682.70.49213480.8120.9470.3340.5970.97795.4
2.68-2.742.70.46213700.8460.9570.3160.5610.86995.3
2.74-2.82.80.36813540.8840.9690.2470.4440.82495.6
2.8-2.872.70.34513730.9020.9740.2330.4180.86595.9
2.87-2.952.70.28613750.9230.980.1940.3470.85896.5
2.95-3.042.70.24713750.9460.9860.1660.2990.85496.2
3.04-3.142.70.21813630.9640.9910.1460.2630.85696.3
3.14-3.252.70.17813860.9710.9930.1190.2150.95396.8
3.25-3.382.70.13713850.9750.9940.0920.1660.94296.9
3.38-3.532.70.11713880.980.9950.0780.1411.21996.9
3.53-3.722.70.09413800.9820.9950.0630.1141.497
3.72-3.952.70.07714280.990.9970.0520.0931.27398
3.95-4.262.70.05514110.9960.9990.0370.0660.95597.7
4.26-4.692.70.04114200.9960.9990.0280.0490.80598.3
4.69-5.362.70.03814090.9970.9990.0260.0460.74498
5.36-6.752.70.04214220.9950.9990.0290.0510.68197.7
6.75-502.70.02614050.99810.0180.0320.54894

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_5127refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30.85 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2454 1292 5.08 %
Rwork0.1901 --
obs0.1929 25437 89.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→30.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4560 0 62 122 4744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014733
X-RAY DIFFRACTIONf_angle_d1.1836387
X-RAY DIFFRACTIONf_dihedral_angle_d11.03645
X-RAY DIFFRACTIONf_chiral_restr0.064664
X-RAY DIFFRACTIONf_plane_restr0.013820
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.60.3806860.24941650X-RAY DIFFRACTION56
2.6-2.720.29331370.24642368X-RAY DIFFRACTION79
2.72-2.860.31381510.24472686X-RAY DIFFRACTION92
2.86-3.040.30561580.25032847X-RAY DIFFRACTION96
3.04-3.280.31961560.2342881X-RAY DIFFRACTION96
3.28-3.60.25451410.2012900X-RAY DIFFRACTION97
3.6-4.120.2211720.17542902X-RAY DIFFRACTION98
4.13-5.190.18031600.1372929X-RAY DIFFRACTION98
5.19-30.850.21511310.16882982X-RAY DIFFRACTION96

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