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- PDB-1o0d: Human Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and ... -

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Basic information

Entry
Database: PDB / ID: 1o0d
TitleHuman Thrombin complexed with a d-Phe-Pro-Arg-type Inhibitor and a C-terminal Hirudin derived exo-site inhibitor
Components
  • Decapeptide Hirudin Analogue
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsBLOOD CLOTTING/HYDROLASE INHIBITOR / ternary complex / thrombin-active-site inhibitor-exo-site inhibitor / BLOOD CLOTTING-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / 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 / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / regulation of cytosolic calcium ion concentration / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / 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 / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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
Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / : / Thrombin light chain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...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
HIRUDIN ANALOGUE / Chem-163 / Prothrombin
Similarity search - Component
Biological speciesHomo sapiens (human)
Hirudo medicinalis (medicinal leech)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsLange, U.E. / Bauke, D. / Hornberger, W. / Mack, H. / Seitz, W. / Hoeffken, H.W.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2003
Title: D-Phe-Pro-Arg type thrombin inhibitors: unexpected selectivity by modification of the P1 moiety
Authors: Lange, U.E. / Bauke, D. / Hornberger, W. / Mack, H. / Seitz, W. / Hoeffken, H.W.
History
DepositionFeb 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 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 1.3Dec 12, 2012Group: Other
Revision 1.4May 25, 2016Group: Source and taxonomy
Revision 1.5Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_residues / software / Item: _software.name
Revision 1.6Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.7Mar 26, 2025Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: Thrombin light chain
H: Thrombin heavy chain
D: Decapeptide Hirudin Analogue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8484
Polymers35,3913
Non-polymers4571
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-4 kcal/mol
Surface area12700 Å2
MethodPISA
2
L: Thrombin light chain
H: Thrombin heavy chain
D: Decapeptide Hirudin Analogue
hetero molecules

L: Thrombin light chain
H: Thrombin heavy chain
D: Decapeptide Hirudin Analogue
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6968
Polymers70,7836
Non-polymers9132
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area11010 Å2
ΔGint-6 kcal/mol
Surface area24450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.880, 71.960, 73.520
Angle α, β, γ (deg.)90.00, 101.06, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein/peptide Thrombin light chain / E.C.3.4.21.5 / Coagulation factor II


Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Organ: blood / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin
#2: Protein Thrombin heavy chain / E.C.3.4.21.5 / Coagulation factor II


Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Organ: blood / Production host: Escherichia coli (E. coli) / References: UniProt: P00734, thrombin
#3: Protein/peptide Decapeptide Hirudin Analogue


Type: Oligopeptide / Class: Anticoagulant, Antithrombotic / Mass: 1514.605 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DECAPEPTIDE / Source: (synth.) Hirudo medicinalis (medicinal leech) / References: HIRUDIN ANALOGUE
#4: Chemical ChemComp-163 / (2-{2-[(5-CARBAMIMIDOYL-1-METHYL-1H-PYRROL-2-YLMETHYL)-CARBAMOYL]-PYRROL-1-YL}- 1-CYCLOHEXYLMETHYL-2-OXO-ETHYLAMINO)-ACETIC ACID


Type: peptide-like / Mass: 456.538 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H32N6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.6 Å3/Da / Density % sol: 52.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: PEG 400, Na-acetate, Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
Method: unknown

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SIEMENS / Detector: CCD / Date: Feb 1, 1998 / Details: goebel mirror
RadiationMonochromator: goebel mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. all: 13607 / Num. obs: 12245 / % possible obs: 90 % / Observed criterion σ(I): 1 / Redundancy: 2.1 % / Biso Wilson estimate: 35.07 Å2 / Rmerge(I) obs: 0.0781 / Rsym value: 0.0781 / Net I/σ(I): 16.042
Reflection shellResolution: 2.44→2.59 Å / Redundancy: 1.23 % / Rmerge(I) obs: 0.3255 / Mean I/σ(I) obs: 1.754 / Num. unique all: 1103 / Rsym value: 0.3255 / % possible all: 49.2
Reflection
*PLUS
Num. measured all: 29541 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Lowest resolution: 2.56 Å / Rmerge(I) obs: 0.32

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Processing

Software
NameClassification
SMARTdata collection
X-GENdata reduction
CNSrefinement
SMARTdata reduction
X-GENdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 889 -random
Rwork0.1993 ---
all-13607 --
obs-11792 6.5 %-
Refinement stepCycle: LAST / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2400 0 33 174 2607
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.40654
Refinement
*PLUS
% reflection Rfree: 6.5 % / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.41

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