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- PDB-1ta2: Crystal structure of thrombin in complex with compound 1 -

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Basic information

Entry
Database: PDB / ID: 1ta2
TitleCrystal structure of thrombin in complex with compound 1
Components
  • Hirudin
  • thrombin
KeywordsHYDROLASE/HYDROLASE INHIBITOR / thrombin inhibitor complex / BLOOD CLOTTING / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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 / serine-type endopeptidase inhibitor 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
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 / 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
Chem-176 / Prothrombin / Hirudin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.3 Å
AuthorsTucker, T.J. / Brady, S.F. / Lumma, W.C. / Lewis, S.D. / Gardel, S.J. / Naylor-Olsen, A.M. / Yan, Y. / Sisko, J.T. / Stauffer, K.J. / Lucas, B.Y. ...Tucker, T.J. / Brady, S.F. / Lumma, W.C. / Lewis, S.D. / Gardel, S.J. / Naylor-Olsen, A.M. / Yan, Y. / Sisko, J.T. / Stauffer, K.J. / Lucas, B.Y. / Lynch, J.J. / Cook, J.J. / Stranieri, M.T. / Holahan, M.A. / Lyle, E.A. / Baskin, E.P. / Chen, I.-W. / Dancheck, K.B. / Krueger, J.A. / Cooper, C.M. / Vacca, J.P.
CitationJournal: J.Med.Chem. / Year: 1998
Title: Design and synthesis of a series of potent and orally bioavailable noncovalent thrombin inhibitors that utilize nonbasic groups in the P1 position
Authors: Tucker, T.J. / Brady, S.F. / Lumma, W.C. / Lewis, S.D. / Gardel, S.J. / Naylor-Olsen, A.M. / Yan, Y. / Sisko, J.T. / Stauffer, K.J. / Lucas, B.Y. / Lynch, J.J. / Cook, J.J. / Stranieri, M.T. ...Authors: Tucker, T.J. / Brady, S.F. / Lumma, W.C. / Lewis, S.D. / Gardel, S.J. / Naylor-Olsen, A.M. / Yan, Y. / Sisko, J.T. / Stauffer, K.J. / Lucas, B.Y. / Lynch, J.J. / Cook, J.J. / Stranieri, M.T. / Holahan, M.A. / Lyle, E.A. / Baskin, E.P. / Chen, I.-W. / Dancheck, K.B. / Krueger, J.A. / Cooper, C.M. / Vacca, J.P.
History
DepositionMay 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: 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 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 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_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: thrombin
B: Hirudin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,9533
Polymers34,4562
Non-polymers4961
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-23 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.81, 72.36, 72.96
Angle α, β, γ (deg.)90.0, 100.9, 90.0
Int Tables number5
Space group name H-MC121

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Components

#1: Protein thrombin / E.C.3.4.21.5 / 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) / Organ: PANCREAS / References: UniProt: P00734, thrombin
#2: Protein/peptide Hirudin


Mass: 1376.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (natural) Hirudo medicinalis (medicinal leech) / References: UniProt: P28504
#3: Chemical ChemComp-176 / 1-(2-AMINO-3,3-DIPHENYL-PROPIONYL)-PYRROLIDINE-3-CARBOXYLIC ACID 2,5-DICHLORO-BENZYLAMIDE


Type: peptide-like / Mass: 496.428 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H27Cl2N3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.66 Å3/Da / Density % sol: 53.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 8000, 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: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 15, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 21542 / % possible obs: 63 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.063 / Rsym value: 0.063

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.3→8 Å / σ(F): 2 /
RfactorNum. reflection
Rwork0.15 -
obs0.151 10171
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2324 0 34 152 2510
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.8

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