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- PDB-1ba8: THROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES -

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Basic information

Entry
Database: PDB / ID: 1ba8
TitleTHROMBIN INHIBITOR WITH A RIGID TRIPEPTIDYL ALDEHYDES
Components
  • (THROMBIN) x 2
  • HIRUGEN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway ...negative regulation of serine-type peptidase activity / positive regulation of lipid kinase activity / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / neutrophil-mediated killing of gram-negative bacterium / regulation of blood coagulation / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of platelet activation / negative regulation of astrocyte differentiation / negative regulation of cytokine production involved in inflammatory response / positive regulation of collagen biosynthetic process / 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 / regulation of cytosolic calcium ion concentration / fibrinolysis / 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 / Cell surface interactions at the vascular wall / lipopolysaccharide binding / negative regulation of proteolysis / 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 / Golgi lumen / positive regulation of protein localization to nucleus / 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 / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, hirudin / Hirudin/antistatin / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Thrombin inhibitor hirudin / Hirudin / Proteinase inhibitor I14, 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 domain profile. / Serine proteases, trypsin family, serine active site. / 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
amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium / Chem-0IT / Prothrombin / Hirudin variant-1
Similarity search - Component
Biological speciesHirudo medicinalis (medicinal leech)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKrishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S.L. / Levy, O.E. / Semple, J.E. / Brunck, T.K.
CitationJournal: Biochemistry / Year: 1998
Title: Highly selective mechanism-based thrombin inhibitors: structures of thrombin and trypsin inhibited with rigid peptidyl aldehydes.
Authors: Krishnan, R. / Zhang, E. / Hakansson, K. / Arni, R.K. / Tulinsky, A. / Lim-Wilby, M.S. / Levy, O.E. / Semple, J.E. / Brunck, T.K.
History
DepositionApr 23, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1May 22, 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 1.3Jul 27, 2011Group: Database references
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.process_site / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THROMBIN
B: THROMBIN
C: HIRUGEN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1275
Polymers35,4383
Non-polymers6892
Water2,846158
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.260, 72.290, 72.990
Angle α, β, γ (deg.)90.00, 100.90, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 2 types, 2 molecules AC

#1: Protein/peptide THROMBIN / / THR-CVS1578


Mass: 4096.534 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin
#3: Protein/peptide HIRUGEN


Mass: 1561.577 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hirudo medicinalis (medicinal leech) / References: UniProt: P01050*PLUS

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Protein / Sugars , 2 types, 2 molecules B

#2: Protein THROMBIN / / THR-CVS1578


Mass: 29780.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: BLOOD / References: UniProt: P00734, thrombin
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 159 molecules

#4: Chemical ChemComp-0IT / amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium / CVS1578


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 467.562 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H31N6O5S
References: amino({(4S)-4-[({(3S)-3-[(benzylsulfonyl)amino]-2-oxopiperidin-1-yl}acetyl)amino]-5-oxopentyl}amino)methaniminium
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C2) OF THE ALDEHYDE GROUP OF THE INHIBITOR ...THE ACTIVE SITE SER 195 IS CLOSE TO THE CARBONYL CARBON (C2) OF THE ALDEHYDE GROUP OF THE INHIBITOR BUT DOES NOT FORM A TETRAHEDRAL INTERMEDIATE

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
124 %PEG80001reservoir
20.1 Mphosphate1reservoir
31 mM1reservoirNaN3

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1995
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 22257 / % possible obs: 61 % / Observed criterion σ(I): 2.5 / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Rsym value: 0.12 / Net I/σ(I): 14
Reflection shellResolution: 1.8→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.25 / % possible all: 38
Reflection
*PLUS
Redundancy: 1.8 % / Num. measured all: 40769 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
% possible obs: 38 % / Rmerge(I) obs: 0.184

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Processing

Software
NameVersionClassification
R-AXISIIdata collection
R-AXISIIdata reduction
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
R-AXISIIdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TMB

1tmb


Resolution: 1.8→7 Å / Cross valid method: THROUGHOUT / σ(F): 4
Details: RESIDUES 148 - 149 IN THE B CHAIN WERE DISORDERED AND ARE NOT INCLUDED IN THE COORDINATES.
RfactorNum. reflection% reflection
Rwork0.152 --
obs-17478 75 %
Displacement parametersBiso mean: 26.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 1.8→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2347 0 46 158 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.040.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.11
X-RAY DIFFRACTIONp_mcangle_it1.81.5
X-RAY DIFFRACTIONp_scbond_it2.62
X-RAY DIFFRACTIONp_scangle_it3.82.5
X-RAY DIFFRACTIONp_plane_restr0.030.03
X-RAY DIFFRACTIONp_chiral_restr0.150.2
X-RAY DIFFRACTIONp_singtor_nbd0.220.6
X-RAY DIFFRACTIONp_multtor_nbd0.310.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.280.6
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor2015
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3020
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS

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