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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 / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / collagen-containing extracellular matrix / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
Similarity search - Function
Epsilon-Thrombin; Chain L / Thrombin light chain domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / Prothrombin/thrombin / Thrombin light chain / Thrombin light chain domain superfamily / Thrombin light chain / Kringle domain / Kringle ...Epsilon-Thrombin; Chain L / Thrombin light chain domain / Plasminogen Kringle 4 / Plasminogen Kringle 4 / 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 / Few Secondary Structures / Irregular / 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
D-Phe-Pro-Arg-CH2Cl / Chem-0G6 / Prothrombin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
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.
History
DepositionNov 30, 1997Processing site: BNL
Revision 1.0Jun 17, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 27, 2013Group: Other
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_name_com.entity_id / _pdbx_database_status.process_site / _pdbx_molecule.asym_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)97,0388
Polymers95,2824
Non-polymers1,7574
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18810 Å2
ΔGint-34 kcal/mol
Surface area34590 Å2
MethodPISA
Unit cell
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-MP41212
Components on special symmetry positions
IDModelComponents
11A-24-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.90024, -0.43536, -0.00555), (-0.43381, 0.89797, -0.07391), (0.03716, -0.06413, -0.99725)
Vector: 178.65675, 42.02666, 32.13877)

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Components

#1: Protein MEIZOTHROMBIN / DESF1


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


Mass: 29772.422 Da / Num. of mol.: 2 / Fragment: F2/THROMBIN DOMAIN / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: BLOOD / Tissue: BLOOD PLASMA / References: UniProt: P00735, thrombin
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-0G6 / D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide / PPACK / PPACK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 453.986 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H34ClN6O3 / References: D-Phe-Pro-Arg-CH2Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % 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
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
117 mg/mlprotein1drop
21-4 %PEG40001drop
30.25 Mammonium sulfate1drop
532-34 %ammonium sulfate1reservoir
60.25 M1reservoirNH42PO4
4PPACK1drop10:1 molar excess

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Mar 1, 1996 / Details: 0.3 MM COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→42.3 Å / Num. obs: 31648 / % possible obs: 88 % / Observed criterion σ(I): 0.5 / Rmerge(I) obs: 0.12 / Rsym value: 0.12 / Net I/σ(I): 5.7
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.19 / % possible all: 60
Reflection shell
*PLUS
% possible obs: 60 %

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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
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THROMBIN

Resolution: 3.2→7 Å / Data cutoff high absF: 99999999 / Data cutoff low absF: 0.0001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -10 %RANDOM
Rwork0.205 ---
obs0.205 30519 84 %-
Refinement stepCycle: LAST / Resolution: 3.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6698 0 116 87 6901
Software
*PLUS
Name: X-PLOR / Version: 3.84 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
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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