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- PDB-11yh: D189F thrombin inhibited with D-Phe-Pro-Phe-Chloromethylketone -

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Basic information

Entry
Database: PDB / ID: 11yh
TitleD189F thrombin inhibited with D-Phe-Pro-Phe-Chloromethylketone
Components
  • Thrombin heavy chain
  • Thrombin light chain
KeywordsBLOOD CLOTTING / serine protease / inhibitor
Function / homology
Function and homology information


negative regulation of astrocyte differentiation / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / Platelet Aggregation (Plug Formation) / Defective F8 cleavage by thrombin ...negative regulation of astrocyte differentiation / thrombospondin receptor activity / thrombin / thrombin-activated receptor signaling pathway / Defective factor XII causes hereditary angioedema / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / Platelet Aggregation (Plug Formation) / Defective F8 cleavage by thrombin / positive regulation of collagen biosynthetic process / Fibrin formation / negative regulation of platelet activation / negative regulation of blood coagulation / negative regulation of fibrinolysis / positive regulation of blood coagulation / negative regulation of proteolysis / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / fibrinolysis / Gamma-carboxylation of protein precursors / Amplification and propagation of coagulation cascade / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Initiation of coagulation cascade / regulation of cytosolic calcium ion concentration / negative regulation of cytokine production involved in inflammatory response / Regulation of clotting cascade / Regulation of Complement cascade / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of release of sequestered calcium ion into cytosol / Cell surface interactions at the vascular wall / growth factor activity / Peptide ligand-binding receptors / response to wounding / lipopolysaccharide binding / platelet activation / positive regulation of protein localization to nucleus / Golgi lumen / blood coagulation / 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 / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / Dengue Virus-Host Interactions / antimicrobial humoral immune response mediated by antimicrobial peptide / blood microparticle / extracellular matrix / G alpha (q) signalling events / cell surface receptor signaling pathway / receptor ligand activity / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / proteolysis / 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. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFriet, T. / Mohammed, B.M. / Korolev, S. / Di Cera, E.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL049413, HL139554, HL147821 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM133893 United States
Department of Energy (DOE, United States)KP1607011 United States
CitationJournal: J.Thromb.Haemost. / Year: 2026
Title: Structural analysis of the primary specificity of thrombin.
Authors: Friet, T. / Mikhail, G. / Mohammed, B.M. / Pelc, L.A. / Dei Rossi, A. / Korolev, S. / Di Cera, E.
History
DepositionMar 18, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thrombin light chain
C: Thrombin light chain
B: Thrombin heavy chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0856
Polymers74,1974
Non-polymers8882
Water2,198122
1
A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5423
Polymers37,0982
Non-polymers4441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-15 kcal/mol
Surface area12590 Å2
MethodPISA
2
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5423
Polymers37,0982
Non-polymers4441
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-11 kcal/mol
Surface area12670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.801, 161.744, 50.332
Angle α, β, γ (deg.)90.000, 90.528, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein/peptide Thrombin light chain


Mass: 5641.175 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734
#2: Protein Thrombin heavy chain


Mass: 31457.119 Da / Num. of mol.: 2 / Mutation: D519F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F2 / Production host: Mesocricetus auratus (golden hamster) / References: UniProt: P00734
#3: Chemical ChemComp-A1DFL / D-phenylalanyl-N-[(2S,3S)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]-L-prolinamide


Mass: 443.966 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30ClN3O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium acetate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1.540562 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Apr 3, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.540562 Å / Relative weight: 1
ReflectionResolution: 2.2→21.25 Å / Num. obs: 35743 / % possible obs: 98.5 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 9.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsDiffraction-ID% possible all
2.2-2.283.20.2943.353577199.8
2.28-2.373.30.2683.873574199.9
2.37-2.473.40.2394.423574199.9
2.47-2.63.50.2155.233574199.8
2.6-2.763.60.1836.243574199.6
2.76-2.973.70.1268.093574199.5
2.97-3.273.90.09310.783574199.5
3.27-3.723.70.08415.853574199.3
3.72-4.653.40.06719.243574197.4
4.65-21.253.50.05718.873574191.3

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419+SVNrefinement
CrysalisProdata scaling
CrysalisProdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→21.25 Å / SU ML: 0.2936 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.7142
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2513 1995 5.59 %
Rwork0.1993 33725 -
obs0.2022 35720 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.92 Å2
Refinement stepCycle: LAST / Resolution: 2.2→21.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 60 122 4874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724878
X-RAY DIFFRACTIONf_angle_d0.94526580
X-RAY DIFFRACTIONf_chiral_restr0.0539674
X-RAY DIFFRACTIONf_plane_restr0.0077844
X-RAY DIFFRACTIONf_dihedral_angle_d16.51021844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.33441410.26012441X-RAY DIFFRACTION99.85
2.26-2.320.28721480.2372412X-RAY DIFFRACTION99.96
2.32-2.380.27411430.22352448X-RAY DIFFRACTION99.92
2.38-2.460.2581440.22722419X-RAY DIFFRACTION99.88
2.46-2.550.2961430.22152417X-RAY DIFFRACTION99.81
2.55-2.650.27421480.22462476X-RAY DIFFRACTION99.62
2.65-2.770.30891340.21562410X-RAY DIFFRACTION99.57
2.77-2.920.2741470.21342422X-RAY DIFFRACTION99.42
2.92-3.10.28791460.21632416X-RAY DIFFRACTION99.65
3.1-3.340.28121480.20222430X-RAY DIFFRACTION99.42
3.34-3.670.21921410.19042426X-RAY DIFFRACTION99.38
3.67-4.20.21021400.16472399X-RAY DIFFRACTION97.73
4.2-5.280.18551340.14772254X-RAY DIFFRACTION92.45
5.28-21.250.2051380.18082355X-RAY DIFFRACTION95.04

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