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- PDB-1ny2: Human alpha thrombin inhibited by RPPGF and hirugen -

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Basic information

Entry
Database: PDB / ID: 1ny2
TitleHuman alpha thrombin inhibited by RPPGF and hirugen
Components
  • Hirugen
  • Inhibitor peptide RPPGF
  • thrombin Heavy chain
  • thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / thrombosis / retro binding / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of cell adhesion / 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 ...negative regulation of cell adhesion / 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 / cysteine-type endopeptidase inhibitor activity / 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 / platelet alpha granule lumen / Regulation of Complement cascade / acute-phase response / positive regulation of receptor signaling pathway via JAK-STAT / Cell surface interactions at the vascular wall / Post-translational protein phosphorylation / lipopolysaccharide binding / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / hormone activity / 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 / vasodilation / Platelet degranulation / heparin binding / regulation of cell shape / Thrombin signalling through proteinase activated receptors (PARs) / positive regulation of protein phosphorylation / positive regulation of cytosolic calcium ion concentration / positive regulation of cell growth / : / G alpha (i) signalling events / G alpha (q) signalling events / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of apoptotic process / inflammatory response / 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 / zinc ion binding / plasma membrane
Similarity search - Function
HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily ...HMW kininogen / Kininogen-type cystatin domain / Kininogen-type cystatin domain profile. / : / Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Hirudin / Proteinase inhibitor I14, hirudin / Thrombin inhibitor 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 / 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
Prothrombin / Kininogen-1 / Hirudin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKrishnan, R. / Tulinsky, A. / Schmaier, A.H. / Hasan, A.A. / Warnock, M. / Srikanth, S. / Mahdi, F.
CitationJournal: Am.J.Physiol.Heart Circ.Physiol. / Year: 2003
Title: Mechanisms of Arg-Pro-Pro-Gly-Phe inhibition of thrombin.
Authors: Hasan, A.A. / Warnock, M. / Nieman, M. / Srikanth, S. / Mahdi, F. / Krishnan, R. / Tulinsky, A. / Schmaier, A.H.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Mar 25, 2015Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.6Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
1: thrombin light chain
2: thrombin Heavy chain
3: Hirugen
4: Inhibitor peptide RPPGF


Theoretical massNumber of molelcules
Total (without water)35,8144
Polymers35,8144
Non-polymers00
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.15, 104.97, 45.18
Angle α, β, γ (deg.)90, 90, 90
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: light chain A / Source method: isolated from a natural source / Details: alpha thrombin catalytic domain / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein thrombin Heavy chain / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: heavy chain B / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#3: Protein/peptide Hirugen


Mass: 1363.399 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P28504
#4: Protein/peptide Inhibitor peptide RPPGF


Mass: 573.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized / References: UniProt: P01042*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
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: 53.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG 4000, ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 25K, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
123.5 %PEG40001reservoir
20.1 Msodium acetate1reservoirpH4.6
30.2 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 11, 1997 / Details: yale mirrors
RadiationMonochromator: yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 23504 / Num. obs: 17158 / % possible obs: 73 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 1.5 / Rmerge(I) obs: 0.068
Reflection shellResolution: 2.1→2.3 Å / % possible all: 0.5
Reflection
*PLUS
% possible obs: 73 %

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Processing

Software
NameClassification
AMoREphasing
PROLSQrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DIT

1dit


Resolution: 2.3→8 Å / σ(F): 3 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rwork0.202 -
all0.202 -
obs-16037
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2503 0 0 51 2554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d0.047
X-RAY DIFFRACTIONp_mcangle_it0.057

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