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- PDB-1bml: COMPLEX OF THE CATALYTIC DOMAIN OF HUMAN PLASMIN AND STREPTOKINASE -

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Basic information

Entry
Database: PDB / ID: 1bml
TitleCOMPLEX OF THE CATALYTIC DOMAIN OF HUMAN PLASMIN AND STREPTOKINASE
Components
  • PLASMIN
  • STREPTOKINASE
KeywordsBLOOD CLOTTING / HUMAN PLASMIN / STREPTOKINASE
Function / homology
Function and homology information


plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / tissue remodeling / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases ...plasmin / trans-synaptic signaling by BDNF, modulating synaptic transmission / tissue remodeling / Signaling by PDGF / positive regulation of fibrinolysis / negative regulation of cell-cell adhesion mediated by cadherin / protein antigen binding / Dissolution of Fibrin Clot / biological process involved in interaction with symbiont / Activation of Matrix Metalloproteinases / collagen catabolic process / extracellular matrix disassembly / negative regulation of cell-substrate adhesion / negative regulation of fibrinolysis / apolipoprotein binding / positive regulation of blood vessel endothelial cell migration / fibrinolysis / Degradation of the extracellular matrix / platelet alpha granule lumen / serine-type peptidase activity / Schaffer collateral - CA1 synapse / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / kinase binding / blood coagulation / Platelet degranulation / protein-folding chaperone binding / protease binding / endopeptidase activity / extracellular matrix / blood microparticle / serine-type endopeptidase activity / external side of plasma membrane / protein domain specific binding / signaling receptor binding / glutamatergic synapse / enzyme binding / cell surface / proteolysis / : / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Ubiquitin-like (UB roll) - #150 / Ubiquitin-like (UB roll) - #180 / Streptokinase / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. ...Ubiquitin-like (UB roll) - #150 / Ubiquitin-like (UB roll) - #180 / Streptokinase / Staphylokinase / Staphylokinase/Streptokinase superfamily / Staphylokinase/Streptokinase family / Peptidase S1A, plasmin / divergent subfamily of APPLE domains / : / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Ubiquitin-like (UB roll) / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin family, serine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Roll / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Plasminogen / Streptokinase C
Similarity search - Component
Biological speciesHomo sapiens (human)
Streptococcus dysgalactiae subsp. equisimilis (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.9 Å
AuthorsWang, X. / Zhang, X.C.
CitationJournal: Science / Year: 1998
Title: Crystal structure of the catalytic domain of human plasmin complexed with streptokinase.
Authors: Wang, X. / Lin, X. / Loy, J.A. / Tang, J. / Zhang, X.C.
History
DepositionMay 25, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 2, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PLASMIN
B: PLASMIN
C: STREPTOKINASE
D: STREPTOKINASE


Theoretical massNumber of molelcules
Total (without water)136,9574
Polymers136,9574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PLASMIN
D: STREPTOKINASE


Theoretical massNumber of molelcules
Total (without water)68,4782
Polymers68,4782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-10 kcal/mol
Surface area26030 Å2
MethodPISA
3
A: PLASMIN
C: STREPTOKINASE


Theoretical massNumber of molelcules
Total (without water)68,4782
Polymers68,4782
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-9 kcal/mol
Surface area26010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.030, 125.050, 86.790
Angle α, β, γ (deg.)90.00, 105.41, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999983, 0.005749, -0.000648), (-0.005418, -0.969859, -0.243605), (-0.002029, -0.243598, 0.969874)66.09162, 162.42328, 20.10509
2given(-0.999965, 0.005811, 0.005953), (-0.007125, -0.9676, -0.252386), (0.004294, -0.25242, 0.967608)65.82504, 162.15196, 20.4755

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Components

#1: Protein PLASMIN


Mass: 27319.402 Da / Num. of mol.: 2 / Fragment: CATALYTIC DOMAIN / Mutation: S741A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P00747, plasmin
#2: Protein STREPTOKINASE


Mass: 41158.949 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Streptococcus dysgalactiae subsp. equisimilis (bacteria)
Species: Streptococcus dysgalactiae / Strain: subsp. equisimilis / References: UniProt: P00779
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: 2.9 Å3/Da / Density % sol: 57 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140 mg/mlprotein1drop
21.0 Msodium citrate1reservoir
30.2 MHEPES1reservoir
41 mMmagnesium chloride1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Aug 1, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→45.4 Å / Num. obs: 33424 / % possible obs: 91.34 % / Redundancy: 1.9 % / Biso Wilson estimate: 47.7 Å2 / Rsym value: 0.053 / Net I/σ(I): 11.25
Reflection shellResolution: 2.9→3 Å / Redundancy: 1.43 % / Mean I/σ(I) obs: 2.17 / Rsym value: 0.252 / % possible all: 80.27
Reflection
*PLUS
% possible obs: 91.3 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 80.3 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
SAINTdata scaling
SAINTdata reduction
MLPHAREphasing
X-PLOR3.8refinement
RefinementMethod to determine structure: MIR / Resolution: 2.9→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0 / Details: A BULK SOLVENT CORRECTION WAS APPLIED.
RfactorNum. reflection% reflectionSelection details
Rfree0.291 3328 9.12 %RANDOM
Rwork0.201 ---
obs0.201 33304 91.34 %-
Displacement parametersBiso mean: 45.6 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8940 0 0 0 8940
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.513
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.77
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.79
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
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.9→3.03 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.391 349 7.69 %
Rwork0.313 3323 -
obs--80.86 %
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.77
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.79

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