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- PDB-1rtf: COMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHA... -

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Basic information

Entry
Database: PDB / ID: 1rtf
TitleCOMPLEX OF BENZAMIDINE WITH THE CATALYTIC DOMAIN OF HUMAN TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR [(TC)-T-PA]
Components(TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR) x 2
KeywordsSERINE PROTEASE / FIBRINOLYTIC ENZYMES
Function / homology
Function and homology information


t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis ...t-plasminogen activator / prevention of polyspermy / trans-synaptic signaling by BDNF, modulating synaptic transmission / Signaling by PDGF / negative regulation of plasminogen activation / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / platelet-derived growth factor receptor signaling pathway / negative regulation of fibrinolysis / serine protease inhibitor complex / fibrinolysis / negative regulation of proteolysis / secretory granule / phosphoprotein binding / protein modification process / Schaffer collateral - CA1 synapse / apical part of cell / blood coagulation / response to hypoxia / signaling receptor binding / serine-type endopeptidase activity / glutamatergic synapse / cell surface / proteolysis / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site ...Tissue plasminogen activator / Fibronectin type I domain / Fibronectin, type I / Fibronectin type-I domain signature. / Fibronectin type-I domain profile. / Fibronectin type 1 domain / EGF-like domain / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / 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
BENZAMIDINE / PHOSPHATE ION / Tissue-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.3 Å
AuthorsBode, W. / Lamba, D.
CitationJournal: J.Mol.Biol. / Year: 1996
Title: The 2.3 A crystal structure of the catalytic domain of recombinant two-chain human tissue-type plasminogen activator
Authors: Lamba, D. / Bauer, M. / Huber, R. / Fischer, S. / Rudolph, R. / Kohnert, U. / Bode, W.
History
DepositionNov 10, 1995Processing site: BNL
Revision 1.0Jan 11, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR
B: TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4944
Polymers30,2792
Non-polymers2152
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-5 kcal/mol
Surface area11410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.200, 59.200, 136.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein/peptide TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR / (TC)-T-PA


Mass: 2121.343 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: t-plasminogen activator
#2: Protein TWO CHAIN TISSUE PLASMINOGEN ACTIVATOR / (TC)-T-PA


Mass: 28157.883 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00750, t-plasminogen activator
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 40 %
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
13 mg/mlprotein1drop
210 mM1dropKH2PO4
310 mMbenzamidine1drop
40.2 MHEPES1reservoir
520 %(v/v)ethanol1reservoircan be replaced by isopropanol

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 12894 / % possible obs: 99.8 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.066
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. measured all: 65287
Reflection shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å / % possible obs: 97.4 % / Rmerge(I) obs: 0.333

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection
Rfree0.265 -
Rwork0.184 -
obs0.184 11836
Displacement parametersBiso mean: 31.4 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 9 56 1990
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
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
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.64

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