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- PDB-1vzq: Complex of thrombin with designed inhibitor 7165 -

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Basic information

Entry
Database: PDB / ID: 1vzq
TitleComplex of thrombin with designed inhibitor 7165
Components
  • HIRUDIN VARIANT-2
  • THROMBIN HEAVY
  • THROMBIN LIGHT
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / BLOOD COAGULATION / PLASMA / CALCIUM-BINDING / GLYCOPROTEIN / SERINE PROTEASE / 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
Chem-SHY / Prothrombin / Hirudin variant-2 / Hirudin-2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
HIRUDO MEDICINALIS (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsShaerer, K. / Morgenthaler, M. / Seiler, P. / Diederich, F. / Banner, D.W. / Tschopp, T. / Obst-Sander, U.
Citation
Journal: Helv.Chim.Acta / Year: 2004
Title: Enantiomerically Pure Thrombin Inhibitors for Exploring the Molecular-Recognition Features of the Oxyanion Hole
Authors: Schaerer, K. / Morgenthaler, M. / Seiler, P. / Diederich, F. / Banner, D.W. / Tschopp, T. / Obst-Sander, U.
#1: Journal: Protein Expr.Purif. / Year: 1997
Title: Stable Expression and Purification of a Secreted Human Recombinant Prethrombin-2 and its Activation to Thrombin
Authors: Russo, G. / Gast, A. / Schlaeger, E.J. / Angiolillo, A. / Pietropaolo, C.
History
DepositionMay 24, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 20, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_PDB_ins_code / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_PDB_ins_code / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: THROMBIN HEAVY
I: HIRUDIN VARIANT-2
L: THROMBIN LIGHT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8626
Polymers33,3503
Non-polymers5123
Water7,350408
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)70.900, 71.400, 72.400
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-2109-

HOH

21I-2010-

HOH

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Components

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Protein , 1 types, 1 molecules H

#1: Protein THROMBIN HEAVY / COAGULATION FACTOR II


Mass: 28750.086 Da / Num. of mol.: 1 / Fragment: SERINE PROTEASE DOMAIN, RESIDUES 364-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P00734, thrombin

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Protein/peptide , 2 types, 2 molecules IL

#2: Protein/peptide HIRUDIN VARIANT-2 / HIRUDIN IIB


Mass: 1411.465 Da / Num. of mol.: 1 / Fragment: C-TERMINAL PEPTIDE, RESIDUES 62-72 / Source method: obtained synthetically / Details: CHEMICALLY SYNTHESISED / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945, UniProt: P28504*PLUS
#3: Protein/peptide THROMBIN LIGHT / COAGULATION FACTOR II


Mass: 3188.627 Da / Num. of mol.: 1 / Fragment: RESIDUES 334-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): OVARY / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P00734, thrombin

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Non-polymers , 4 types, 411 molecules

#4: Chemical ChemComp-SHY / 4-[(3AS,4R,7R,8AS,8BR)-2-(1,3-BENZODIOXOL-5-YLMETHYL)-7-HYDROXY-1,3-DIOXODECAHYDROPYRROLO[3,4-A]PYRROLIZIN-4-YL]BENZENECARBOXIMIDAMIDE


Mass: 448.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H24N4O5
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 43 %
Crystal growpH: 7.4 / Details: PH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 3, 2003 / Details: OSMIC MIRRORS
RadiationMonochromator: OSMICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. obs: 43087 / % possible obs: 82.2 % / Observed criterion σ(I): -3 / Redundancy: 7.11 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.98
Reflection shellResolution: 1.54→1.63 Å / Redundancy: 6.93 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 8.56 / % possible all: 83.9

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Processing

Software
NameVersionClassification
CNX2002refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OYT

1oyt


Resolution: 1.54→18.55 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: CHYMOTRYPSIN NUMBERING RATHER THAN SEQUENTIAL SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN W.BODE ET AL., 1989, EMBO J.8, 3467-3475. THE STRUCTURE OF ...Details: CHYMOTRYPSIN NUMBERING RATHER THAN SEQUENTIAL SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSIN W.BODE ET AL., 1989, EMBO J.8, 3467-3475. THE STRUCTURE OF 1OYT.PDB WAS TAKEN AS STARTING POINT FOR THE REFINEMENT. APART FROM THE INHIBITOR AND A FEW WATER MOLECULES THE TWO STRUCTURES ARE THE SAME. WATER S339 HAS ELECTRON DENSITY, BUT IS NOT RELIABLE ON GEOMETRIC GROUNDS. OTHER WATER MOLECULES WITH B OVER 50 SHOULD NOT BE TRUSTED. THE INHIBITOR AND GLU 192 HAVE GOOD DENSITY, SO THE SHORT HYDROGEN BOND BETWEEN THEM IS RELIABLE
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2155 5 %RANDOM
Rwork0.181 ---
obs-43087 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.95 Å2 / ksol: 0.32 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-1.31 Å2
2---1.82 Å20 Å2
3---1.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.54→18.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 35 408 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.261.5
X-RAY DIFFRACTIONc_mcangle_it1.892
X-RAY DIFFRACTIONc_scbond_it1.892
X-RAY DIFFRACTIONc_scangle_it2.672.5
LS refinement shellResolution: 1.54→1.6 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.223 5 %
Rwork0.216 -
obs-79.4 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: 7165.TPX

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