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

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Basic information

Entry
Database: PDB / ID: 1mkx
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 / collagen-containing extracellular matrix / 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. / Kringle domain profile. ...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
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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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
Water6,828379
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 area2330 Å2
ΔGint-10 kcal/mol
Surface area13110 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
3
L: ALPHA-THROMBIN
H: ALPHA-THROMBIN
K: PRETHROMBIN-2

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


Theoretical massNumber of molelcules
Total (without water)141,9956
Polymers141,9956
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area13020 Å2
ΔGint-48 kcal/mol
Surface area46340 Å2
MethodPISA
4
K: PRETHROMBIN-2

K: PRETHROMBIN-2


Theoretical massNumber of molelcules
Total (without water)70,9792
Polymers70,9792
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area3090 Å2
ΔGint-2 kcal/mol
Surface area25380 Å2
MethodPISA
5
H: ALPHA-THROMBIN
K: PRETHROMBIN-2

H: ALPHA-THROMBIN
K: PRETHROMBIN-2


Theoretical massNumber of molelcules
Total (without water)130,5244
Polymers130,5244
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area8360 Å2
ΔGint-28 kcal/mol
Surface area44920 Å2
MethodPISA
6
L: ALPHA-THROMBIN


Theoretical massNumber of molelcules
Total (without water)5,7351
Polymers5,7351
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.520, 87.990, 101.650
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 (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 (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 (cattle) / References: UniProt: P00735, thrombin
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growpH: 5.8
Details: 38% AMMONIUM SULFATE, 0.25M AMMONIUM PHOSPHATE, PH 5.8, 1% POLYETHYLENE GLYCOL 4000 (DROP ONLY).
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
17 mg/mlprotein1drop
20.25 Mammonium phosphate1droppH6.0
338 %ammonium sulfate1reservoir
40.25 Mammonium phosphate1reservoirpH5.8

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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: 1.9→7 Å / Num. obs: 47039 / % possible obs: 75 % / Observed criterion σ(I): 0 / Rsym value: 0.101
Reflection
*PLUS
Num. measured all: 142959 / Rmerge(I) obs: 0.101

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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: 2.2→7 Å
RfactorNum. reflection
Rfree0.255 -
Rwork0.187 -
obs0.187 34872
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4636 0 0 379 5015
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.28
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_d1.84
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
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg2.28
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.84

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