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- PDB-12it: Thrombin inhibited with D-Phe-Pro-Gln-Chloromethylketone -

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Basic information

Entry
Database: PDB / ID: 12it
TitleThrombin inhibited with D-Phe-Pro-Gln-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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsFriet, T. / Mohammed, B.M. / Sukumar, N. / 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
DepositionApr 7, 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
B: Thrombin heavy chain
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,47110
Polymers74,1324
Non-polymers1,3386
Water5,819323
1
A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7355
Polymers37,0662
Non-polymers6693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-20 kcal/mol
Surface area12360 Å2
MethodPISA
2
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7355
Polymers37,0662
Non-polymers6693
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-21 kcal/mol
Surface area12360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.228, 86.170, 73.693
Angle α, β, γ (deg.)90.000, 90.213, 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

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Protein/peptide / Protein / Sugars , 3 types, 6 molecules ACBD

#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: 31425.033 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
#4: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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 , 3 types, 327 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-A1DFV / D-phenylalanyl-N-[(2S,3S)-6-amino-1-chloro-2-hydroxy-6-oxohexan-3-yl]-L-prolinamide


Mass: 424.922 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29ClN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.94 Å3/Da / Density % sol: 36.57 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 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: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.91989 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 2, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91989 Å / Relative weight: 1
ReflectionResolution: 1.68→34.76 Å / Num. obs: 62689 / % possible obs: 99 % / Redundancy: 6 % / Biso Wilson estimate: 16.21 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.189 / Rpim(I) all: 0.084 / Rrim(I) all: 0.207 / Χ2: 0.93 / Net I/σ(I): 6.4
Reflection shellResolution: 1.68→1.77 Å / Redundancy: 6 % / Rmerge(I) obs: 2 / Num. unique obs: 9017 / CC1/2: 0.439 / Rpim(I) all: 0.879 / Rrim(I) all: 2.187 / Χ2: 0.86

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.68→34.76 Å / SU ML: 0.1889 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4902
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2287 2787 4.78 %
Rwork0.1836 55504 -
obs0.1857 58291 92.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.98 Å2
Refinement stepCycle: LAST / Resolution: 1.68→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4482 0 86 323 4891
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00584675
X-RAY DIFFRACTIONf_angle_d0.87736306
X-RAY DIFFRACTIONf_chiral_restr0.0564663
X-RAY DIFFRACTIONf_plane_restr0.0072807
X-RAY DIFFRACTIONf_dihedral_angle_d15.57411821
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.68-1.710.2928340.2593928X-RAY DIFFRACTION30.32
1.71-1.740.2807960.25921618X-RAY DIFFRACTION55.15
1.74-1.770.31261240.24992491X-RAY DIFFRACTION83.36
1.77-1.810.32461320.25082929X-RAY DIFFRACTION98.84
1.81-1.850.271490.22112942X-RAY DIFFRACTION96.99
1.85-1.890.28351300.212985X-RAY DIFFRACTION99.68
1.89-1.940.22331490.20322903X-RAY DIFFRACTION97.51
1.94-1.990.25771570.19032976X-RAY DIFFRACTION99.27
1.99-2.050.24541370.19422950X-RAY DIFFRACTION98.53
2.05-2.120.26541470.19262921X-RAY DIFFRACTION98.24
2.12-2.190.22741670.18582940X-RAY DIFFRACTION99.74
2.19-2.280.21341530.17962953X-RAY DIFFRACTION98.79
2.28-2.380.2491470.17562984X-RAY DIFFRACTION98.86
2.38-2.510.21821450.18482956X-RAY DIFFRACTION99.14
2.51-2.670.2551470.18882971X-RAY DIFFRACTION99.27
2.67-2.870.24841560.19073001X-RAY DIFFRACTION99.59
2.87-3.160.24131390.19133002X-RAY DIFFRACTION99.46
3.16-3.620.23151420.17093006X-RAY DIFFRACTION99.87
3.62-4.560.18821720.14552988X-RAY DIFFRACTION99.68
4.56-34.760.17881640.17123060X-RAY DIFFRACTION99.88

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