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- PDB-1a0h: THE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE... -

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Entry
Database: PDB / ID: 1a0h
TitleTHE X-RAY CRYSTAL STRUCTURE OF PPACK-MEIZOTHROMBIN DESF1: KRINGLE/THROMBIN AND CARBOHYDRATE/KRINGLE/THROMBIN INTERACTIONS AND LOCATION OF THE LINKER CHAIN
Components(MEIZOTHROMBIN) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SERINE PROTEASE / COAGULATION / THROMBIN / PROTHROMBIN / MEIZOTHROMBIN / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homologyKringle / Serine proteases, trypsin family, serine active site / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Trypsin / Kringle domain / Kringle superfamily / Thrombin light chain domain superfamily / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Thrombin light chain / Serine proteases, trypsin domain ...Kringle / Serine proteases, trypsin family, serine active site / Vitamin K-dependent carboxylation/gamma-carboxyglutamic (GLA) domain / Trypsin / Kringle domain / Kringle superfamily / Thrombin light chain domain superfamily / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Thrombin light chain / Serine proteases, trypsin domain / Serine proteases, trypsin family, histidine active site / Kringle, conserved site / Kringle-like fold / Peptidase S1, PA clan / Prothrombin/thrombin / Peptidase S1A, chymotrypsin family / Thrombin light chain / Vitamin K-dependent carboxylation domain. / Kringle domain signature. / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Regulation of Complement cascade / Platelet Aggregation (Plug Formation) / Thrombin signalling through proteinase activated receptors (PARs) / G alpha (q) signalling events / Peptide ligand-binding receptors / Cell surface interactions at the vascular wall / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Gamma-carboxyglutamic acid-rich (GLA) domain / Serine proteases, trypsin family, histidine active site. / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Intrinsic Pathway of Fibrin Clot Formation / Gla domain profile. / Serine proteases, trypsin domain profile. / Kringle domain profile. / Serine proteases, trypsin family, serine active site. / fibrinogen binding / blood coagulation, fibrin clot formation / protein polymerization / 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 / neutrophil mediated killing of gram-negative bacterium / negative regulation of cytokine production involved in inflammatory response / negative regulation of astrocyte differentiation / positive regulation of collagen biosynthetic process / positive regulation of blood coagulation / positive regulation of release of sequestered calcium ion into cytosol / enzyme activator activity / fibrinolysis / lipopolysaccharide binding / negative regulation of proteolysis / acute-phase response / positive regulation of protein localization to nucleus / positive regulation of reactive oxygen species metabolic process / platelet activation / heparin binding / positive regulation of phosphatidylinositol 3-kinase signaling / positive regulation of cell growth / regulation of cell shape / regulation of gene expression / antimicrobial humoral immune response mediated by antimicrobial peptide / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / external side of plasma membrane / proteolysis / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / extracellular space / Prothrombin
Function and homology information
Specimen sourceBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 3.2 Å resolution
AuthorsMartin, P.D. / Malkowski, M.G. / Box, J. / Esmon, C.T. / Edwards, B.F.P.
CitationJournal: Structure / Year: 1997
Title: New insights into the regulation of the blood clotting cascade derived from the X-ray crystal structure of bovine meizothrombin des F1 in complex with PPACK.
Authors: Martin, P.D. / Malkowski, M.G. / Box, J. / Esmon, C.T. / Edwards, B.F.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 30, 1997 / Release: Jun 17, 1998
RevisionDateData content typeGroupProviderType
1.0Jun 17, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelAtomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
1.3Nov 16, 2011Structure modelAtomic model
1.4Feb 27, 2013Structure modelOther

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MEIZOTHROMBIN
B: MEIZOTHROMBIN
D: MEIZOTHROMBIN
E: MEIZOTHROMBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,07410
Polyers95,2824
Non-polymers1,7936
Water1,56787
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)18810
ΔGint (kcal/M)-34
Surface area (Å2)34590
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)186.150, 186.150, 120.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP 41 21 2

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Components

#1: Protein/peptide MEIZOTHROMBIN / DESF1


Mass: 17868.338 Da / Num. of mol.: 2 / Fragment: F2/THROMBIN DOMAIN / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: BLOOD / Tissue: BLOOD PLASMA / References: UniProt: P00735, thrombin
#2: Protein/peptide MEIZOTHROMBIN / DESF1


Mass: 29772.422 Da / Num. of mol.: 2 / Fragment: F2/THROMBIN DOMAIN / Source: (natural) Bos taurus (cattle) / Genus: Bos / Organ: BLOOD / Tissue: BLOOD PLASMA / References: UniProt: P00735, thrombin
#3: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK / PPACK


Mass: 453.986 Da / Num. of mol.: 2 / Formula: C21H34ClN6O3

about BIRD dictionary

PRD-IDPRD_000020
ClassInhibitor
NameD-Phe-Pro-Arg-CH2Cl
TypePeptide-like
#4: Chemical
ChemComp-NAG / N-ACETYL-D-GLUCOSAMINE


Mass: 221.208 Da / Num. of mol.: 4 / Formula: C8H15NO6 / N-Acetylglucosamine
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Formula: H2O / Water
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS D-PHE-PRO-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER525 (CHAINS B,E) FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS363 (CHAINS B,E)

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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: 5.4 / Density percent sol: 76 %
Crystal growpH: 8
Details: 17 MG/ML PROTEIN, 2% PEG4000, .25 M AMMONIUM PHOSPHATE, PH 8.0, 33% SATURATED AMMONIUM SULFATE
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
components of the solutions
*PLUS

Crystal ID: 1

IDConcCommon nameSol IDChemical formulaDetails
117 mg/mlproteindrop
21-4 %PEG4000drop
30.25 Mammonium sulfatedrop
532-34 %ammonium sulfatereservoir
60.25 MreservoirNH42PO4
4PPACKdrop10:1 molar excess

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Data collection

DiffractionMean temperature: 273 kelvins
SourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Details: 0.3 MM COLLIMATOR / Detector: AREA DETECTOR / Collection date: Mar 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionD resolution high: 3.2 Å / D resolution low: 42.3 Å / Number obs: 31648 / Observed criterion sigma I: 0.5 / Rmerge I obs: 0.12 / Rsym value: 0.12 / NetI over sigmaI: 5.7 / Percent possible obs: 88
Reflection shellRmerge I obs: 0.19 / Highest resolution: 3.2 Å / Lowest resolution: 3.3 Å / MeanI over sigI obs: 1.8 / Rsym value: 0.19 / Percent possible all: 6
Reflection shell
*PLUS
Percent possible obs: 6

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Processing

Software
NameVersionClassification
XENGENdata collection
SCALEKdata reduction
X-PLOR3.84model building
X-PLOR3.84refinement
XENGENdata reduction
SCALEKdata scaling
X-PLOR3.84phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THROMBIN

R Free selection details: RANDOM / Data cutoff high absF: 99999999 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / Sigma F: 1
Least-squares processR factor R free: 0.242 / R factor R work: 0.205 / R factor obs: 0.205 / Highest resolution: 3.2 Å / Lowest resolution: 7 Å / Number reflection obs: 30519 / Percent reflection R free: 1 / Percent reflection obs: 84
Refine hist #LASTHighest resolution: 3.2 Å / Lowest resolution: 7 Å
Number of atoms included #LASTProtein: 6698 / Nucleic acid: 0 / Ligand: 116 / Solvent: 87 / Total: 6901
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refine LS restraints
*PLUS
Refine IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_d1.96
X-RAY DIFFRACTIONx_dihedral_angle_deg26.06
X-RAY DIFFRACTIONx_improper_angle_deg1.72

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