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- PDB-1mh0: Crystal structure of the anticoagulant slow form of thrombin -

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Basic information

Entry
Database: PDB / ID: 1mh0
TitleCrystal structure of the anticoagulant slow form of thrombin
ComponentsProthrombin
KeywordsBLOOD CLOTTING / thrombin / allostery / sodium binding / serine protease
Function / homology
Function and homology information


cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin ...cytolysis by host of symbiont cells / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / thrombin-activated receptor signaling pathway / negative regulation of astrocyte differentiation / regulation of blood coagulation / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / neutrophil-mediated killing of gram-negative bacterium / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / ligand-gated ion channel signaling pathway / positive regulation of collagen biosynthetic process / negative regulation of platelet activation / negative regulation of blood coagulation / positive regulation of blood coagulation / negative regulation of fibrinolysis / regulation of cytosolic calcium ion concentration / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / negative regulation of proteolysis / negative regulation of cytokine production involved in inflammatory response / Peptide ligand-binding receptors / Regulation of Complement cascade / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / growth factor activity / lipopolysaccharide binding / 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 / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / regulation of cell shape / heparin binding / Thrombin signalling through proteinase activated receptors (PARs) / : / positive regulation of cell growth / blood microparticle / G alpha (q) signalling events / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor ligand activity / endoplasmic reticulum lumen / signaling receptor binding / serine-type endopeptidase activity / positive regulation of cell population proliferation / calcium ion binding / proteolysis / extracellular space / 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. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPineda, A.O. / Savvides, S. / Waksman, G. / Di Cera, E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of the anticoagulant slow form of thrombin
Authors: Pineda, A.O. / Savvides, S. / Waksman, G. / Di Cera, E.
History
DepositionAug 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Nov 13, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prothrombin
B: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4584
Polymers66,0162
Non-polymers4422
Water2,000111
1
A: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2292
Polymers33,0081
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prothrombin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2292
Polymers33,0081
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.530, 72.890, 161.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein Prothrombin / E.C.3.4.21.5 / Alpha-thrombin / coagulation factor II


Mass: 33007.875 Da / Num. of mol.: 2 / Mutation: R77aA
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: blood / Plasmid: HPC4-pNUT / Organ (production host): kidney / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): kidney cells / References: UniProt: P00734, thrombin
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H2O
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: 2.7 Å3/Da / Density % sol: 54.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PEG 2000-Monomethyl ether, Tris-Cl, pH 7.6, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 25 ℃ / pH: 7.4 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15.6 mg/mlmutant1drop
250 mMcholine chloride1drop
320 mMTris1droppH7.4
414 %PEG2000 MME1reservoir
50.1 MTris1reservoirpH7.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 23, 2002 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 16577 / % possible obs: 90.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Biso Wilson estimate: -0.5 Å2
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. measured all: 70807 / Rmerge(I) obs: 0.111
Reflection shell
*PLUS
% possible obs: 78 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 1.8

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1PPB

1ppb


Resolution: 2.8→29.75 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The mismatched residues R75, K145, K240 (A chain) and K145 (B chain) were modelled as Alanines due to poor electron density
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1056 6.9 %RANDOM
Rwork0.219 ---
all0.2191 16543 --
obs0.2191 15367 84.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 20.6116 Å2 / ksol: 0.320496 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-15.87 Å20 Å20 Å2
2---1.17 Å20 Å2
3----14.71 Å2
Refine analyzeLuzzati coordinate error free: 0.48 Å / Luzzati sigma a free: 0.74 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 28 111 4605
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.432 123 6.3 %
Rwork0.375 1837 -
obs-16577 66 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5NAG.PARAMNAG.TOPO
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92

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