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- PDB-1mkw: THE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND ... -

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Basic information

Entry
Database: PDB / ID: 1mkw
TitleTHE CO-CRYSTAL STRUCTURE OF UNLIGANDED BOVINE ALPHA-THROMBIN AND PRETHROMBIN-2: MOVEMENT OF THE YPPW SEGMENT AND ACTIVE SITE RESIDUES UPON LIGAND BINDING
Components
  • (ALPHA-THROMBIN) x 2
  • PRETHROMBIN-2
KeywordsCOMPLEX (BLOOD COAGULATION/PROENZYME) / COMPLEX (BLOOD COAGULATION-PROENZYME) / THROMBIN / PRETHROMBIN-2 / PLASMA / SERINE PROTEASE / COMPLEX (BLOOD COAGULATION-PROENZYME) complex
Function / homology
Function and homology information


fibrinogen binding / thrombin / protein polymerization / positive regulation of blood coagulation / acute-phase response / platelet activation / : / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMalkowski, M.G. / Edwards, B.F.P.
Citation
Journal: Protein Sci. / Year: 1997
Title: The co-crystal structure of unliganded bovine alpha-thrombin and prethrombin-2: movement of the Tyr-Pro-Pro-Trp segment and active site residues upon ligand binding.
Authors: Malkowski, M.G. / Martin, P.D. / Guzik, J.C. / Edwards, B.F.
#1: Journal: Biochemistry / Year: 1996
Title: Bovine Thrombin Complexed with an Uncleavable Analog of Residues 7-19 of Fibrinogen a Alpha: Geometry of the Catalytic Triad and Interactions of the P1', P2', and P3' Substrate Residues
Authors: Martin, P.D. / Malkowski, M.G. / Dimaio, J. / Konishi, Y. / Ni, F. / Edwards, B.F.
#2: Journal: Protein Sci. / Year: 1994
Title: The Isomorphous Structures of Prethrombin2, Hirugen-, and Ppack-Thrombin: Changes Accompanying Activation and Exosite Binding to Thrombin
Authors: Vijayalakshmi, J. / Padmanabhan, K.P. / Mann, K.G. / Tulinsky, A.
History
DepositionMar 13, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: ALPHA-THROMBIN
H: ALPHA-THROMBIN
K: PRETHROMBIN-2


Theoretical massNumber of molelcules
Total (without water)70,9973
Polymers70,9973
Non-polymers00
Water3,693205
1
L: ALPHA-THROMBIN
H: ALPHA-THROMBIN


Theoretical massNumber of molelcules
Total (without water)35,5082
Polymers35,5082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-10 kcal/mol
Surface area12880 Å2
MethodPISA
2
K: PRETHROMBIN-2


Theoretical massNumber of molelcules
Total (without water)35,4901
Polymers35,4901
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.580, 88.550, 101.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHERE ARE TWO INDEPENDENT COMPLEXES IN THE ASYMMETRIC UNIT. COMPLEX I IS ALPHA THROMBIN, AND COMPLEX II IS PRETHROMBIN-2. ALPHA THROMBIN IN COMPLEX I HAS BEEN ASSIGNED CHAIN INDICATORS *L* AND *H*, AND PRETHROMBIN-2 IN COMPLEX II HAS BEEN ASSIGNED CHAIN INDICATOR *K*.

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Components

#1: Protein/peptide ALPHA-THROMBIN


Mass: 5735.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00735, thrombin
#2: Protein ALPHA-THROMBIN


Mass: 29772.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00735, thrombin
#3: Protein PRETHROMBIN-2


Mass: 35489.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00735, thrombin
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ...CHYMOTRYPSINOGEN NUMBERING (RATHER THAN SEQUENTIAL) SYSTEM IS USED, BASED ON THE TOPOLOGICAL ALIGNMENT WITH THE STRUCTURE OF CHYMOTRYPSINOGEN (H.BRANDSTETTER ET AL., 1992, J.MOL.BIOL., V. 226, 1085).

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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: 2.76 Å3/Da / Density % sol: 55.4 %
Crystal growpH: 4.6
Details: 24% POLYETHYLENE GLYCOL 2000, 0.1M SODIUM ACETATE, PH 4.6, 0.2M AMMONIUM SULFATE
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 7.3 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
250 mM1dropNaPO4
3100 mM1dropNaCl
424 %PEG20001reservoir
50.1 Msodium acetate1reservoir
60.2 Mammonium sulfate1reservoir
70.1 %1reservoirNaN3

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→7 Å / Num. obs: 44681 / % possible obs: 79 % / Observed criterion σ(I): 0 / Rsym value: 0.072
Reflection
*PLUS
Num. measured all: 90801 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.5 Å / % possible obs: 57 %

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Processing

Software
NameClassification
XENGENdata collection
XENGENdata reduction
X-PLORmodel building
X-PLORrefinement
XENGENdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→7 Å
RfactorNum. reflection
Rfree0.282 -
Rwork0.19 -
obs0.19 32058
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 0 205 4841
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.96
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.96

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