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- PDB-1lmw: LMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethy... -

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Basic information

Entry
Database: PDB / ID: 1lmw
TitleLMW U-PA Structure complexed with EGRCMK (GLU-GLY-ARG Chloromethyl Ketone)
Components(UROKINASE-TYPE PLASMINOGEN ACTIVATOR) x 2
KeywordsHydrolase/Hydrolase Inhibitor / FIBRINOLYSIS / TRYPSIN-LIKE SERINE PROTEASE / SERINE PROTEASE / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex ...u-plasminogen activator / regulation of smooth muscle cell-matrix adhesion / urokinase plasminogen activator signaling pathway / regulation of plasminogen activation / regulation of fibrinolysis / regulation of wound healing / protein complex involved in cell-matrix adhesion / regulation of signaling receptor activity / negative regulation of plasminogen activation / serine-type endopeptidase complex / regulation of smooth muscle cell migration / Dissolution of Fibrin Clot / smooth muscle cell migration / plasminogen activation / regulation of cell adhesion mediated by integrin / tertiary granule membrane / negative regulation of fibrinolysis / regulation of cell adhesion / specific granule membrane / serine protease inhibitor complex / fibrinolysis / chemotaxis / blood coagulation / regulation of cell population proliferation / response to hypoxia / positive regulation of cell migration / external side of plasma membrane / serine-type endopeptidase activity / focal adhesion / Neutrophil degranulation / cell surface / signal transduction / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / : / Kringle-like fold / EGF-like domain profile. ...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 / 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
GLU-GLY-ARG-CHLOROMETHYL KETONE / Chem-0GJ / Urokinase-type plasminogen activator
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSpraggon, G.S. / Phillips, C. / Nowak, U.K. / Ponting, C.P. / Saunders, D. / Dobson, C.M. / Stuart, D.I. / Jones, E.Y.
CitationJournal: Structure / Year: 1995
Title: The crystal structure of the catalytic domain of human urokinase-type plasminogen activator.
Authors: Spraggon, G. / Phillips, C. / Nowak, U.K. / Ponting, C.P. / Saunders, D. / Dobson, C.M. / Stuart, D.I. / Jones, E.Y.
History
DepositionJul 26, 1995Processing site: BNL
Revision 1.0Jan 29, 1996Provider: 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 1.4Oct 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
B: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
C: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
D: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1656
Polymers62,3734
Non-polymers7922
Water00
1
A: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
B: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5823
Polymers31,1872
Non-polymers3961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area820 Å2
ΔGint-4 kcal/mol
Surface area12080 Å2
MethodPISA
2
C: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
D: UROKINASE-TYPE PLASMINOGEN ACTIVATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5823
Polymers31,1872
Non-polymers3961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area980 Å2
ΔGint-4 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.700, 176.700, 54.400
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein/peptide UROKINASE-TYPE PLASMINOGEN ACTIVATOR / LMW U-PA


Mass: 2708.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00749, u-plasminogen activator
#2: Protein UROKINASE-TYPE PLASMINOGEN ACTIVATOR / LMW U-PA


Mass: 28478.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P00749, u-plasminogen activator
#3: Chemical ChemComp-0GJ / L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide / EGRCMK


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 395.862 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28ClN6O5 / Details: HUMAN LOW MOLECULAR WEIGHT U-PA / References: GLU-GLY-ARG-CHLOROMETHYL KETONE
Compound detailsTHE STRUCTURE IS THAT OF THE ACTIVE, TWO CHAIN FORM OF THE ENZYME.
Has protein modificationY
Nonpolymer detailsTHE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT ...THE UNBOUND FORM OF THE INHIBITOR IS GLU-GLY-ARG-CHLOROMETHYLKETONE. UPON REACTION WITH PROTEIN IT FORMS TWO COVALENT BONDS: 1) A COVALENT BOND TO OG SER 195 FORMING A HEMIKETAL AR7 AND 2) A COVALENT BOND TO NE2 OF HIS 57
Sequence detailsTHE RESIDUES IN THE STRUCTURE ARE NUMBERED, AS IS CONVENTIONAL WITH SERINE PROTEASES, AS ...THE RESIDUES IN THE STRUCTURE ARE NUMBERED, AS IS CONVENTIONAL WITH SERINE PROTEASES, AS TOPOLOGICAL EQUIVALENTS TO CHYMOTRYPSIN.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.5 %
Crystal
*PLUS
Density % sol: 60 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
113-14 %PEG80001reservoir
20.2 M1reservoirLi2SO4

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A
DetectorType: FUJI / Detector: IMAGE PLATE / Date: 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 15684 / % possible obs: 70 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.111
Reflection
*PLUS
Highest resolution: 2.5 Å / Num. measured all: 54540 / Rmerge(I) obs: 0.111

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Processing

Software
NameClassification
DENZOdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→30 Å
Details: THE 23 RESIDUES OF THE SHORT A CHAIN IN EACH SUBUNIT ARE HIGHLY MOBILE. RESIDUES 147 - 152 (1 - 6 AS CHYMOTRYPSIN EQUIVALENTS) ARE MODELED IN DENSITY, 153 AND 154 FITTED TENTATIVELY IN WEAK ...Details: THE 23 RESIDUES OF THE SHORT A CHAIN IN EACH SUBUNIT ARE HIGHLY MOBILE. RESIDUES 147 - 152 (1 - 6 AS CHYMOTRYPSIN EQUIVALENTS) ARE MODELED IN DENSITY, 153 AND 154 FITTED TENTATIVELY IN WEAK DENSITY WHILE THE REMAINDER ARE ABSENT.
RfactorNum. reflection
Rwork0.224 -
obs0.224 15684
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4043 0 50 0 4093
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
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_deg
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
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 2

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