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- PDB-1bqy: Plasminogen activator (TSV-PA) from snake venom -

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Basic information

Entry
Database: PDB / ID: 1bqy
TitlePlasminogen activator (TSV-PA) from snake venom
ComponentsPLASMINOGEN ACTIVATOR
KeywordsHYDROLASE/HYDROLASE INHIBITOR / FIBRINOLYSIS / PLASMINOGEN ACTIVATOR / SERINE PROTEINASE / SNAKE VENOM / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / BLOOD CLOTTING
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / secretory granule / toxin activity / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine 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 / Peptidase S1, PA clan, chymotrypsin-like fold ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, histidine 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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / : / Venom plasminogen activator TSV-PA
Similarity search - Component
Biological speciesViridovipera stejnegeri (Stejneger's pit viper)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsParry, M.A.A. / Bode, W.
CitationJournal: Structure / Year: 1998
Title: The crystal structure of the novel snake venom plasminogen activator TSV-PA: a prototype structure for snake venom serine proteinases.
Authors: Parry, M.A. / Jacob, U. / Huber, R. / Wisner, A. / Bon, C. / Bode, W.
History
DepositionAug 20, 1998Processing site: BNL
Revision 1.0Aug 20, 1999Provider: 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 1.3Feb 27, 2013Group: Other
Revision 1.4Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PLASMINOGEN ACTIVATOR
B: PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0604
Polymers51,2682
Non-polymers7922
Water2,918162
1
B: PLASMINOGEN ACTIVATOR
hetero molecules

A: PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0604
Polymers51,2682
Non-polymers7922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_646-x+1,y-1/2,-z+3/21
2
A: PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0302
Polymers25,6341
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0302
Polymers25,6341
Non-polymers3961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.290, 67.420, 163.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein PLASMINOGEN ACTIVATOR / TSV-PA


Mass: 25634.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Viridovipera stejnegeri (Stejneger's pit viper)
Organ: VENOM GLAND / Plasmid: PET / Production host: Escherichia coli (E. coli) / References: PIR: A57290, UniProt: Q91516*PLUS
#2: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28ClN6O5
Details: CHLOROMETHYLKETONE INHIBITOR COVALENTLY BOUND TO THE ACTIVE SITE SER 195 AND HIS 57
References: GLU-GLY-ARG-CHLOROMETHYL KETONE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CMK-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57. RESIDUE GLU OF THE INHIBITOR IS MODELED WITH ZERO OCCUPANCY.

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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: 2.6 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
pH: 4.3 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17.5 mg/mlprotein1drop
20.1 MNa acetate1reservoir
30.2 M1reservoirMgCl2
425 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1997 / Details: MIRRORS
RadiationMonochromator: CU FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 17988 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.444 / % possible all: 82.1
Reflection
*PLUS
Num. measured all: 91942
Reflection shell
*PLUS
% possible obs: 82.1 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
CCP4(SCALA)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PTB

3ptb


Resolution: 2.5→30 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 861 5 %RANDOM
Rwork0.178 ---
obs0.178 17215 95.7 %-
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 50 162 3806
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_deg1.87
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
LS refinement shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.59 Å / Rfactor Rwork: 0.352

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