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- PDB-2pks: Thrombin in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2pks
TitleThrombin in complex with inhibitor
Components
  • (Thrombin heavy chain ...) x 2
  • Hirudin
  • Thrombin light chain
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Inhibitor complex / thrombin inhibitor / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...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 / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / 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 / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / lipopolysaccharide binding / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / 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 / serine-type endopeptidase inhibitor activity / antimicrobial humoral immune response mediated by antimicrobial peptide / blood coagulation / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / positive regulation of cell growth / regulation of cell shape / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / positive regulation of cell population proliferation / calcium ion binding / 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 ...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
Chem-G44 / Prothrombin / Hirudin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsXue, Y.
CitationJournal: Org.Biomol.Chem. / Year: 2007
Title: Design, synthesis and biological evaluation of thrombin inhibitors based on a pyridine scaffold.
Authors: Blomberg, D. / Fex, T. / Xue, Y. / Brickmann, K. / Kihlberg, J.
History
DepositionApr 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,5546
Polymers33,1874
Non-polymers3672
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.942, 71.843, 70.778
Angle α, β, γ (deg.)90.000, 100.230, 90.000
Int Tables number5
Space group name H-MC121
Detailsthe monomer present in the asymmetric unit is the biological unit

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Components

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Protein/peptide , 2 types, 2 molecules AD

#1: Protein/peptide Thrombin light chain


Mass: 3188.627 Da / Num. of mol.: 1 / Fragment: Residues 335-361 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734
#4: Protein/peptide Hirudin


Mass: 1291.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized. / References: UniProt: P28504

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Thrombin heavy chain ... , 2 types, 2 molecules BC

#2: Protein Thrombin heavy chain fragment


Mass: 17070.738 Da / Num. of mol.: 1 / Fragment: Residues 364-510 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734
#3: Protein Thrombin heavy chain fragment


Mass: 11636.286 Da / Num. of mol.: 1 / Fragment: Residues 518-619 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P00734

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Non-polymers , 3 types, 49 molecules

#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-G44 / 4-({[4-(3-METHYLBENZOYL)PYRIDIN-2-YL]AMINO}METHYL)BENZENECARBOXIMIDAMIDE


Mass: 344.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H20N4O
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.753.3
22.753.3
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 27% PEG8000, 0.1M SODIUM PHOSPHATE, PH 7.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: CCD
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→69.673 Å / Num. all: 25416 / Num. obs: 10962 / % possible obs: 91.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 6.7
Reflection shellResolution: 2.5→2.57 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 1.8 / Num. unique all: 823 / Rsym value: 0.423 / % possible all: 93.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→69.67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.897 / SU B: 9.701 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.135 / ESU R Free: 0.336 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 502 4.8 %RANDOM
Rwork0.185 ---
all0.188 ---
obs-10553 87.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.912 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-2.72 Å2
2---2.35 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→69.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 27 47 2401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0222414
X-RAY DIFFRACTIONr_angle_refined_deg1.9151.9853262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5285282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12723.451113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.15315426
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8511520
X-RAY DIFFRACTIONr_chiral_restr0.1250.2334
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021844
X-RAY DIFFRACTIONr_nbd_refined0.250.21103
X-RAY DIFFRACTIONr_nbtor_refined0.3150.21559
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2133
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.229
X-RAY DIFFRACTIONr_mcbond_it1.0171.51422
X-RAY DIFFRACTIONr_mcangle_it1.89422294
X-RAY DIFFRACTIONr_scbond_it2.52831046
X-RAY DIFFRACTIONr_scangle_it4.0464.5968
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 33 -
Rwork0.245 707 -
obs-740 84.67 %

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