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

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Basic information

Entry
Database: PDB / ID: 11vg
TitleD189F thrombin 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: 2.13 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
DepositionMar 13, 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)75,4898
Polymers74,1974
Non-polymers1,2924
Water5,026279
1
A: Thrombin light chain
B: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7444
Polymers37,0982
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-15 kcal/mol
Surface area13170 Å2
MethodPISA
2
C: Thrombin light chain
D: Thrombin heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7444
Polymers37,0982
Non-polymers6462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-15 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.150, 165.521, 50.475
Angle α, β, γ (deg.)90.000, 89.992, 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: 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
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M BIS-TRIS pH 6.5, 20% w/v Polyethylene glycol monomethyl ether 5,000

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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: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 15, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.13→33.65 Å / Num. obs: 40358 / % possible obs: 98.3 % / Redundancy: 6 % / Biso Wilson estimate: 10.98 Å2 / CC1/2: 0.93 / Rmerge(I) obs: 0.43 / Rpim(I) all: 0.186 / Rrim(I) all: 0.47 / Χ2: 0.89 / Net I/σ(I): 3.2 / Num. measured all: 240634
Reflection shellResolution: 2.13→2.25 Å / % possible obs: 97.3 % / Redundancy: 5.8 % / Rmerge(I) obs: 1.395 / Num. measured all: 33790 / Num. unique obs: 5855 / CC1/2: 0.374 / Rpim(I) all: 0.604 / Rrim(I) all: 1.523 / Χ2: 0.84 / Net I/σ(I) obs: 1.5

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Processing

Software
NameVersionClassification
PHENIX2.0_5936refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.13→33.65 Å / SU ML: 0.2848 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 24.7955
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2612 1951 4.96 %
Rwork0.2056 37373 -
obs0.2084 39324 95.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.21 Å2
Refinement stepCycle: LAST / Resolution: 2.13→33.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 84 279 5133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00694992
X-RAY DIFFRACTIONf_angle_d1.0226736
X-RAY DIFFRACTIONf_chiral_restr0.0717694
X-RAY DIFFRACTIONf_plane_restr0.0072862
X-RAY DIFFRACTIONf_dihedral_angle_d16.96281920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.180.30011280.25171941X-RAY DIFFRACTION70.25
2.18-2.240.33951340.26782370X-RAY DIFFRACTION85.4
2.24-2.310.28141320.25412657X-RAY DIFFRACTION95.35
2.31-2.380.35071640.24422743X-RAY DIFFRACTION97.65
2.38-2.470.30291510.23992675X-RAY DIFFRACTION97.62
2.47-2.570.27821290.23522759X-RAY DIFFRACTION98
2.57-2.680.27121270.22842787X-RAY DIFFRACTION98.02
2.68-2.820.30361280.22832770X-RAY DIFFRACTION98.24
2.82-30.28941160.21652769X-RAY DIFFRACTION98.53
3-3.230.27021340.21412784X-RAY DIFFRACTION98.08
3.23-3.560.2271520.18752745X-RAY DIFFRACTION98.91
3.56-4.070.22541830.16282731X-RAY DIFFRACTION99.12
4.07-5.130.21031230.14462821X-RAY DIFFRACTION99.26
5.13-33.650.19371500.17932821X-RAY DIFFRACTION99.56
Refinement TLS params.Method: refined / Origin x: 16.322406169684 Å / Origin y: 40.371359452131 Å / Origin z: 0.03121201372925 Å
111213212223313233
T-0.018125544683387 Å2-0.01643319272067 Å2-0.0064323232024223 Å2--0.01452835956015 Å2-0.01858690860357 Å2---0.0035199335673604 Å2
L0.060676773649588 °2-0.0092071715865823 °2-0.018259340071065 °2-0.068741034380389 °20.028714769672122 °2--0.02320344142856 °2
S-0.042266037699295 Å °-0.028621509200172 Å °-0.014017102871595 Å °-0.0012692001019456 Å °0.03422431252331 Å °-0.009964467950111 Å °0.015445964956267 Å °0.054216395443859 Å °-0.14841040489043 Å °
Refinement TLS groupSelection details: all

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