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- PDB-1z71: thrombin and P2 pyridine N-oxide inhibitor complex structure -

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Basic information

Entry
Database: PDB / ID: 1z71
Titlethrombin and P2 pyridine N-oxide inhibitor complex structure
Components
  • Hirudin IIIB'
  • thrombin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / thrombin inhibitor complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


positive regulation of lipid kinase activity / 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 / 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 / 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 / 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 / Regulation of Complement cascade / acute-phase response / 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 / 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 / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / 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
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 ...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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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
L17 / Prothrombin / Hirudin-2 / Hirudin-3B'
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsNantermet, P.G. / Burgey, C.S. / Robinson, K.A. / Pellicore, J.M. / Newton, C.L. / Deng, J.Z. / Lyle, T.A. / Selnick, H.G. / Lewis, S.D. / Lucas, B.J. ...Nantermet, P.G. / Burgey, C.S. / Robinson, K.A. / Pellicore, J.M. / Newton, C.L. / Deng, J.Z. / Lyle, T.A. / Selnick, H.G. / Lewis, S.D. / Lucas, B.J. / Krueger, J.A. / Miller-Stein, C. / White, R.B. / Wong, B. / McMasters, D.R. / Wallace, A.A. / Lynch Jr., J.J. / Yan, Y. / Chen, Z. / Kuo, L. / Gardell, S.J. / Shafer, J.A. / Vacca, J.P.
CitationJournal: BIOORG.MED.CHEM.LETT. / Year: 2005
Title: P(2) pyridine N-oxide thrombin inhibitors: a novel peptidomimetic scaffold
Authors: Nantermet, P.G. / Burgey, C.S. / Robinson, K.A. / Pellicore, J.M. / Newton, C.L. / Deng, J.Z. / Selnick, H.G. / Lewis, S.D. / Lucas, B.J. / Krueger, J.A. / Miller-Stein, C. / White, R.B. / ...Authors: Nantermet, P.G. / Burgey, C.S. / Robinson, K.A. / Pellicore, J.M. / Newton, C.L. / Deng, J.Z. / Selnick, H.G. / Lewis, S.D. / Lucas, B.J. / Krueger, J.A. / Miller-Stein, C. / White, R.B. / Wong, B. / McMasters, D.R. / Wallace, A.A. / Lynch Jr., J.J. / Yan, Y. / Chen, Z. / Kuo, L. / Gardell, S.J. / Shafer, J.A. / Vacca, J.P. / Lyle, T.A.
History
DepositionMar 23, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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 1.3Dec 12, 2012Group: Other
Revision 1.4Mar 13, 2013Group: Other
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software
Revision 1.6Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999 SEQUENCE According to authors, Hirugen was chemically synthesized.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: thrombin
B: Hirudin IIIB'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0123
Polymers34,5142
Non-polymers4971
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.97, 71.49, 72.26
Angle α, β, γ (deg.)90., 100.5, 90.
Int Tables number5
Space group name H-MC121

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Components

#1: Protein thrombin / Coagulation factor II


Mass: 33079.965 Da / Num. of mol.: 1 / Fragment: alpha-thrombin / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734, thrombin
#2: Protein/peptide Hirudin IIIB'


Mass: 1434.477 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Occurs naturally in medicinal leech Hirudo medicinalis
Source: (natural) Hirudo medicinalis (medicinal leech), (synth.) Hirudo medicinalis (medicinal leech)
References: UniProt: P28511, UniProt: P28504*PLUS
#3: Chemical ChemComp-L17 / L17 / 2-(3-CHLORO-6-{[2,2-DIFLUORO-2-(1-OXIDOPYRIDIN-2-YL)ETHYL]AMINO}-1-OXIDOPYRIDIN-2-YL)-N-[1-(3-CHLOROPHENYL)ETHYL]ACETAMIDE


Mass: 497.322 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20Cl2F2N4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: peg8k, sodium phosphate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Sep 19, 2002
RadiationMonochromator: Yale mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 32524 / Num. obs: 32360 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.047 / Rsym value: 0.047
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3 % / Rmerge(I) obs: 0.219 / Mean I/σ(I) obs: 4 / Num. unique all: 3053 / Rsym value: 0.219 / % possible all: 94

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Processing

Software
NameClassification
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.8→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 3173 -random
Rwork0.223 ---
obs0.223 31786 98 %-
all-32524 --
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2337 0 33 194 2564
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0074
X-RAY DIFFRACTIONc_angle_deg1.35

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