1ddj

CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN

Method: X-RAY DIFFRACTION D_max: 149.2 Å Quality: REASONABLE

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

PLASMINOGEN

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 564–810	Fragment：CATALYTIC DOMAIN Mutation：S741A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, SODIUM CHLORIDE, ISOPROPANOL, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.267
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 564–810	Fragment：CATALYTIC DOMAIN Mutation：S741A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, SODIUM CHLORIDE, ISOPROPANOL, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.267
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 564–810	Fragment：CATALYTIC DOMAIN Mutation：S741A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, SODIUM CHLORIDE, ISOPROPANOL, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.267
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 564–810	Fragment：CATALYTIC DOMAIN Mutation：S741A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG 4000, SODIUM CHLORIDE, ISOPROPANOL, ADA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.267

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1DDJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B2I KRINGLE 2 DOMAIN OF HUMAN PLASMINOGEN: NMR SOLUTION STRUCTURE OF TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID (AMCHA) COMPLEX Deposited 1999-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 181–263（83 aa） Fragment：KRINGLE 2 DOMAIN	Mutation：C181T, E182S, C188G	AMH TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 5.1；310 K；Ionic strength (raw mmCIF value) SEE PAPER；Pressure AMBIENT NMR sample composition 90% H2O/10% D2O	Resolution not provided
1BML COMPLEX OF THE CATALYTIC DOMAIN OF HUMAN PLASMIN AND STREPTOKINASE Deposited 1999-05-25	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 561–810（250 aa） Fragment：CATALYTIC DOMAIN Chain B 561–810（250 aa） Fragment：CATALYTIC DOMAIN	Mutation：S741A Mutation：S741A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.90 Å R-free 0.291
1BML COMPLEX OF THE CATALYTIC DOMAIN OF HUMAN PLASMIN AND STREPTOKINASE Deposited 1999-05-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 561–810（250 aa） Fragment：CATALYTIC DOMAIN	Mutation：S741A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.90 Å R-free 0.291
1BML COMPLEX OF THE CATALYTIC DOMAIN OF HUMAN PLASMIN AND STREPTOKINASE Deposited 1999-05-25	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 561–810（250 aa） Fragment：CATALYTIC DOMAIN	Mutation：S741A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8.0	Resolution 2.90 Å R-free 0.291
1BUI Structure of the ternary microplasmin-staphylokinase-microplasmin complex: a proteinase-cofactor-substrate complex in action Deposited 1998-09-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 561–810（250 aa） Fragment：Peptidase S1 catalytic domain Chain B 561–810（250 aa） Fragment：Peptidase S1 catalytic domain	Not recorded	0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 2.65 Å R-free 0.287
1CEA THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH EACA (EPSILON-AMINOCAPROIC ACID) Deposited 1995-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 100–187（88 aa） Fragment：KRINGLE 1	Not recorded	ACA 6-AMINOHEXANOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.06 Å
1CEA THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH EACA (EPSILON-AMINOCAPROIC ACID) Deposited 1995-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–187（88 aa） Fragment：KRINGLE 1	Not recorded	ACA 6-AMINOHEXANOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.06 Å
1CEB THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH AMCHA (TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID) Deposited 1995-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–187（88 aa） Fragment：KRINGLE 1	Not recorded	AMH TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.07 Å
1CEB THE STRUCTURE OF THE NON-COVALENT COMPLEX OF RECOMBINANT KRINGLE 1 DOMAIN OF HUMAN PLASMINOGEN WITH AMCHA (TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID) Deposited 1995-12-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 100–187（88 aa） Fragment：KRINGLE 1	Not recorded	AMH TRANS-4-AMINOMETHYLCYCLOHEXANE-1-CARBOXYLIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.07 Å
1HPJ SOLUTION NMR STRUCTURE OF THE HUMAN PLASMINOGEN KRINGLE 1 DOMAIN COMPLEXED WITH 6-AMINOHEXANOIC ACID AT PH 5.3, 310K, DERIVED FROM RANDOMLY GENERATED STRUCTURES USING SIMULATED ANNEALING, 12 STRUCTURES Deposited 1996-08-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 103–181（79 aa） Fragment：KRINGLE 1 DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.3；310 K	Resolution not provided
1HPK SOLUTION NMR STRUCTURE OF THE HUMAN PLASMINOGEN KRINGLE 1 DOMAIN COMPLEXED WITH 6-AMINOHEXANOIC ACID AT PH 5.3, 310K, DERIVED FROM RANDOMLY GENERATED STRUCTURES USING SIMULATED ANNEALING, MINIMIZED AVERAGE STRUCTURE Deposited 1996-08-14	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 103–181（79 aa） Fragment：KRINGLE 1 DOMAIN	Not recorded	ACA 6-AMINOHEXANOIC ACID × 1	SOLUTION NMR NMR measurement conditions pH 5.3；310 K	Resolution not provided
1I5K STRUCTURE AND BINDING DETERMINANTS OF THE RECOMBINANT KRINGLE-2 DOMAIN OF HUMAN PLASMINOGEN TO AN INTERNAL PEPTIDE FROM A GROUP A STREPTOCOCCAL SURFACE PROTEIN Deposited 2001-02-27	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 183–262（80 aa） Fragment：MODIFIED RECOMBINANT KRINGLE-2 DOMAIN Chain B 183–262（80 aa） Fragment：MODIFIED RECOMBINANT KRINGLE-2 DOMAIN	Mutation：C4G/E56D/L72Y Mutation：C4G/E56D/L72Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；298 K；23%(w/v) PEG 3350, 0.1 M Mes, 0.2 M Li2SO4, 2mM CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.262
1KI0 The X-ray Structure of Human Angiostatin Deposited 2001-12-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 100–352（253 aa）	Mutation：N289E	BCN BICINE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；277 K；PEG 20,000, bicine, dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.75 Å R-free 0.263
1KRN STRUCTURE OF KRINGLE 4 AT 4C TEMPERATURE AND 1.67 ANGSTROMS RESOLUTION Deposited 1995-06-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 374–461（88 aa） Fragment：KRINGLE 4 DOMAIN	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions CRYSTALLIZED FROM BASA (BENZYL AMIN SULFONIC ACID) BUT ONLY SULFATE VISIBLE IN THE STRUCTURE.	Resolution 1.67 Å R-free 0.232
1L4D CRYSTAL STRUCTURE OF MICROPLASMINOGEN-STREPTOKINASE ALPHA DOMAIN COMPLEX Deposited 2002-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 562–810（249 aa） Fragment：CATALYTIC DOMAIN, Residues 543-791	Mutation：S741A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Li2SO4, Hepes, Mg Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.K	Resolution 2.30 Å R-free 0.263
1L4D CRYSTAL STRUCTURE OF MICROPLASMINOGEN-STREPTOKINASE ALPHA DOMAIN COMPLEX Deposited 2002-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 562–810（249 aa） Fragment：CATALYTIC DOMAIN, Residues 543-791	Mutation：S741A	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Li2SO4, Hepes, Mg Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.K	Resolution 2.30 Å R-free 0.263
1L4D CRYSTAL STRUCTURE OF MICROPLASMINOGEN-STREPTOKINASE ALPHA DOMAIN COMPLEX Deposited 2002-03-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 562–810（249 aa） Fragment：CATALYTIC DOMAIN, Residues 543-791	Mutation：S741A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Li2SO4, Hepes, Mg Acetate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.K	Resolution 2.30 Å R-free 0.263
1L4Z X-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF MICROPLASMINOGEN WITH ALPHA DOMAIN OF STREPTOKINASE IN THE PRESENCE CADMIUM IONS Deposited 2002-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 563–810（248 aa） Fragment：Catalytic domain, Residues 544-791	Mutation：S741A	CD CADMIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na acetate, cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.262
1L4Z X-RAY CRYSTAL STRUCTURE OF THE COMPLEX OF MICROPLASMINOGEN WITH ALPHA DOMAIN OF STREPTOKINASE IN THE PRESENCE CADMIUM IONS Deposited 2002-03-06	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 563–810（248 aa） Fragment：Catalytic domain, Residues 544-791	Mutation：S741A	CD CADMIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Na acetate, cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.262
1PK4 CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN PLASMINOGEN KRINGLE 4 REFINED AT 1.9-ANGSTROMS RESOLUTION Deposited 1991-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–454（79 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1PKR THE STRUCTURE OF RECOMBINANT PLASMINOGEN KRINGLE 1 AND THE FIBRIN BINDING SITE Deposited 1993-08-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–181（81 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.48 Å
1PMK KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES Deposited 1994-04-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 374–461（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
1PMK KRINGLE-KRINGLE INTERACTIONS IN MULTIMER KRINGLE STRUCTURES Deposited 1994-04-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 374–461（88 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
1QRZ CATALYTIC DOMAIN OF PLASMINOGEN Deposited 1999-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 565–810（246 aa） Fragment：CATALYTIC DOMAIN	Mutation：M585Q, V673M, M788L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, ISOPROPANOL, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.294
1QRZ CATALYTIC DOMAIN OF PLASMINOGEN Deposited 1999-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 565–810（246 aa） Fragment：CATALYTIC DOMAIN	Mutation：M585Q, V673M, M788L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, ISOPROPANOL, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.294
1QRZ CATALYTIC DOMAIN OF PLASMINOGEN Deposited 1999-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 565–810（246 aa） Fragment：CATALYTIC DOMAIN	Mutation：M585Q, V673M, M788L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, ISOPROPANOL, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.294
1QRZ CATALYTIC DOMAIN OF PLASMINOGEN Deposited 1999-06-16	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 565–810（246 aa） Fragment：CATALYTIC DOMAIN	Mutation：M585Q, V673M, M788L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；PEG 4000, ISOPROPANOL, CITRATE, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.294
1RJX Human PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT Deposited 2003-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 564–810（247 aa） Fragment：Serine Protease CATALYTIC DOMAIN	Mutation：K698M, R561A	SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.6；293 K；Li2SO4, Na citrate, pH 5.6, hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.245
1RJX Human PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT Deposited 2003-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain B 564–810（247 aa） Fragment：Serine Protease CATALYTIC DOMAIN	Mutation：K698M, R561A	SO4 SULFATE ION × 192	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.6；293 K；Li2SO4, Na citrate, pH 5.6, hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.245
1RJX Human PLASMINOGEN CATALYTIC DOMAIN, K698M MUTANT Deposited 2003-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain B 564–810（247 aa） Fragment：Serine Protease CATALYTIC DOMAIN	Mutation：K698M, R561A	SO4 SULFATE ION × 48	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 5.6；293 K；Li2SO4, Na citrate, pH 5.6, hanging drop, temperature 293K	Resolution 2.30 Å R-free 0.245
2DOH The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound a to a peptide from the group A streptococcal surface protein PAM Deposited 2006-04-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 100–333（234 aa） Fragment：Kringle 1,Kringle 2 and Kringle 3	Mutation：N289E	DIO 1,4-DIETHYLENE DIOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 8000, 0.1M potassium phosphate (dihydrate), 5% dioxane, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.260
2DOI The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM Deposited 2006-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 100–333（234 aa） Fragment：Kringle 1,Kringle 2 and Kringle 3	Mutation：N289E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.296
2DOI The X-ray crystallographic structure of the angiogenesis inhibitor, angiostatin, bound to a peptide from the group A streptococcus protein PAM Deposited 2006-04-29	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 100–333（234 aa） Fragment：Kringle 1,Kringle 2 and Kringle 3	Mutation：N289E	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；20% PEG 8000, 0.1M potassium phophate (dihydrate), 5% dioxane, soaked in 5mM Pt(C5H5N)2Cl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.10 Å R-free 0.296
2KNF Solution structure and functional characterization of human plasminogen kringle 5 Deposited 2009-08-21	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 480–562（83 aa）	Mutation：A14V	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 50 mM sodium phosphate, 11 mM AMCHA, 2.2 mM rK5, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2L0S Solution Structure of Human Plasminogen Kringle 3 Deposited 2010-07-15	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 272–354（83 aa） Fragment：UNP residues 272-354, Kringle 3 Domain	Mutation：C43S	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR measurement conditions 298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 1.0 mM [U-97% 15N] hPgn rK3-1, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2PK4 THE REFINED STRUCTURE OF THE EPSILON-AMINOCAPROIC ACID COMPLEX OF HUMAN PLASMINOGEN KRINGLE Deposited 1991-07-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 375–454（80 aa）	Not recorded	ACA 6-AMINOHEXANOIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
3UIR Crystal structure of the plasmin-textilinin-1 complex Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 564–810（247 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.17M ammonium sulfate, 25.5% PEG 4000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.78 Å R-free 0.258
3UIR Crystal structure of the plasmin-textilinin-1 complex Deposited 2011-11-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 564–810（247 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.17M ammonium sulfate, 25.5% PEG 4000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.78 Å R-free 0.258
4A5T STRUCTURAL BASIS FOR THE CONFORMATIONAL MODULATION Deposited 2011-10-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain S 20–810（791 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.49 Å R-free 0.250
4CIK plasminogen kringle 1 in complex with inhibitor Deposited 2013-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 101–181（81 aa） Fragment：KRINGLE 1, RESIDUES 101-181	Not recorded	XO3 5-[(2R,4S)-2-(phenylmethyl)piperidin-4-yl]-1,2-oxazol-3-one × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.78 Å R-free 0.292
4DCB Y. pestis Plasminogen Activator Pla in Complex with Human Plasminogen Activation Loop Peptide ALP11 Deposited 2012-01-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 576–585（10 aa）	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；45% (v/v) 2-methyl-2,4-pentanediol (MPD), 0.2 M NH4KH2PO4 and 0.1M NaOAc, pH 5.5, VAPOR DIFFUSION, HANGING DROP	Resolution 2.03 Å R-free 0.232
4DUR The X-ray Crystal Structure of Full-Length type II Human Plasminogen Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–810（791 aa）	Not recorded	CL CHLORIDE ION × 4 K POTASSIUM ION × 1 BCT BICARBONATE ION × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M sodium citrate, 0.2M sodium acetate, polyethylene glycol 1000, polyethylene glycol 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.215
4DUR The X-ray Crystal Structure of Full-Length type II Human Plasminogen Deposited 2012-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 20–810（791 aa）	Not recorded	CL CHLORIDE ION × 3 K POTASSIUM ION × 1 BCT BICARBONATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；277 K；0.1M sodium citrate, 0.2M sodium acetate, polyethylene glycol 1000, polyethylene glycol 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.45 Å R-free 0.215
4DUU The X-ray Crystal Structure of Full-Length type I Human Plasminogen Deposited 2012-02-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–810（791 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；2M sodium formate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 5.20 Å R-free 0.312
5HPG STRUCTURE AND LIGAND DETERMINANTS OF THE RECOMBINANT KRINGLE 5 DOMAIN OF HUMAN PLASMINOGEN Deposited 1997-09-19	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 480–563（84 aa） Fragment：KRINGLE 5 Chain B 480–563（84 aa） Fragment：KRINGLE 5	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；24% (W/V) PEG 8000, 0.1 M NA-HEPES, PH 7.0, 0.15 M LI2(SO4)	Resolution 1.66 Å
5UGD Protease Inhibitor Deposited 2017-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–810（249 aa） Fragment：UNP residues 562-810	Not recorded	89S Nalpha-[trans-4-(aminomethyl)cyclohexane-1-carbonyl]-N-octyl-O-[(pyridin-4-yl)methyl]-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；10 % (w/v) polyethylene glycol 6,000, 4 % (v/v) 2-methyl-2,4-pentanediol, 0.1M (2-(N-morpholino)ethanesulfonic acid)	Resolution 1.38 Å R-free 0.182
5UGG Protease Inhibitor Deposited 2017-01-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 562–810（249 aa） Fragment：UNP residues 562-810	Not recorded	89M Nalpha-[trans-4-(aminomethyl)cyclohexane-1-carbonyl]-N-octyl-O-[(quinolin-2-yl)methyl]-L-tyrosinamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；10 % (w/v) polyethylene glycol 6,000, 4 % (v/v) 2-methyl-2,4-pentanediol, 0.1M (2-(N-morpholino)ethanesulfonic acid)	Resolution 1.20 Å R-free 0.176
6D3X Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma Deposited 2018-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 565–810（246 aa） Fragment：UNP residues 565-810	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG4000, 0.1 M magnesium chloride, 0.1 M sodium citrate	Resolution 1.80 Å R-free 0.216
6D3X Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma Deposited 2018-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 565–810（246 aa） Fragment：UNP residues 565-810	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；21% PEG4000, 0.1 M magnesium chloride, 0.1 M sodium citrate	Resolution 1.80 Å R-free 0.216
6D3Y Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma Deposited 2018-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 564–810（247 aa） Fragment：UNP residues 564-810	Not recorded	SO4 SULFATE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M 2-ethanesulfonic acid, 0.15 M ammonium sulfate, 13% PEG4000	Resolution 1.32 Å R-free 0.213
6D3Z Protease SFTI complex Deposited 2018-04-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 565–810（246 aa） Fragment：UNP residues 565-810	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M sodium acetate, 1 M sodium formate	Resolution 2.00 Å R-free 0.203
6D40 Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma Deposited 2018-04-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 563–810（248 aa） Fragment：UNP residues 563-810	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；15% PEG4000, 0.1 M MES, 0.15 M ammonium sulfate	Resolution 1.43 Å R-free 0.210
6OG4 plasminogen binding group A streptococcal M protein Deposited 2019-04-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 183–264（82 aa） Fragment：Kringle 2 domain (UNP residues 183-264) Chain B 183–264（82 aa） Fragment：Kringle 2 domain (UNP residues 183-264)	Mutation：C169A Mutation：C169A	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1 M HEPES, pH 7.0, 2 M ammonium sulfate	Resolution 1.70 Å R-free 0.220
6Q1U Structure of plasmin and peptide complex Deposited 2019-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 562–810（249 aa）	Not recorded	WMH 1-methyl-1H-1,2,3-triazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM Sodium Citrate, 100 mM MgCl2, 18% PEG 4000	Resolution 2.35 Å R-free 0.287
6Q1U Structure of plasmin and peptide complex Deposited 2019-08-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 562–810（249 aa）	Not recorded	WMH 1-methyl-1H-1,2,3-triazole × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM Sodium Citrate, 100 mM MgCl2, 18% PEG 4000	Resolution 2.35 Å R-free 0.287
6UZ4 Solution structure of AGL55-Kringle 2 complex Deposited 2019-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 185–262（78 aa）	Mutation：C11G, E63D, L79Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] AGL55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM AGL55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6UZ5 Solution structure of KTI55-Kringle 2 complex Deposited 2019-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 185–262（78 aa）	Mutation：C11G, E63D, L79Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.7；298 K；Ionic strength (raw mmCIF value) 20；Pressure 1 NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] KTI55, 1.2 mM Kringle 2, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.0 mM [U-99% 13C; U-99% 15N] Kringle 2, 1.2 mM KTI55, 20 mM [U-2H] Bis-Tris-d19, 2 ug/mL DSS, 2 ug/mL sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
7E50 Crystal structure of human microplasmin in complex with kazal-type inhibitor AaTI Deposited 2021-02-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 564–810（247 aa）	Not recorded	GOL GLYCEROL × 1 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M Ammonium formate, 20 % polyethylene glycol 3350 pH 6.6	Resolution 1.95 Å R-free 0.275
7THS Macrocyclic plasmin inhibitor Deposited 2022-01-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 561–810（250 aa）	Mutation：S760A	I5Y (6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3,13,21-trioxo-2,6,9,14,22-pentaazatetracyclo[23.2.2.2~6,9~.2~15,18~]tritriaconta-1(27),15,17,25,28,30-hexaene-23-carboxamide × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES	Resolution 1.80 Å R-free 0.208
7THS Macrocyclic plasmin inhibitor Deposited 2022-01-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 561–810（250 aa）	Mutation：S760A	I5Y (6S,9R,20R,23S)-N-{[4-(aminomethyl)phenyl]methyl}-20-[(benzenesulfonyl)amino]-3,13,21-trioxo-2,6,9,14,22-pentaazatetracyclo[23.2.2.2~6,9~.2~15,18~]tritriaconta-1(27),15,17,25,28,30-hexaene-23-carboxamide × 1 SO4 SULFATE ION × 3 I5Q (2S)-butane-1,2-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES	Resolution 1.80 Å R-free 0.208
7UAH Macrocyclic plasmin inhibitor Deposited 2022-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 561–810（250 aa）	Mutation：S760A	M63 (6S,9R,19S,22R)-N-{[4-(aminomethyl)phenyl]methyl}-22-[(3-chlorobenzene-1-sulfonyl)amino]-3,12,21-trioxo-2,6,9,13,20-pentaazatetracyclo[22.2.2.2~6,9~.2~14,17~]dotriaconta-1(26),14,16,24,27,29-hexaene-19-carboxamide × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES, 10% 1,2-butanediol	Resolution 1.57 Å R-free 0.192
7UAH Macrocyclic plasmin inhibitor Deposited 2022-03-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 561–810（250 aa）	Mutation：S760A	M63 (6S,9R,19S,22R)-N-{[4-(aminomethyl)phenyl]methyl}-22-[(3-chlorobenzene-1-sulfonyl)amino]-3,12,21-trioxo-2,6,9,13,20-pentaazatetracyclo[22.2.2.2~6,9~.2~14,17~]dotriaconta-1(26),14,16,24,27,29-hexaene-19-carboxamide × 1 SO4 SULFATE ION × 2 NZ5 (2~{R})-butane-1,2-diol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES, 10% 1,2-butanediol	Resolution 1.57 Å R-free 0.192
8F7U Macrocyclic Plasmin Inhibitor Deposited 2022-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 561–810（250 aa）	Mutation：S760A	GGI (5S,8R,18S,21R)-N-{[4-(aminomethyl)phenyl]methyl}-21-[(benzenesulfonyl)amino]-3,11,20-trioxo-2,5,8,12,19-pentaazatetracyclo[21.2.2.2~5,8~.2~13,16~]hentriaconta-1(25),13,15,23,26,28-hexaene-18-carboxamide × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；293 K；14% PEG 4000, 90-140 mM Ammonium sulfate, 100 mM MES	Resolution 1.47 Å R-free 0.189
8F7U Macrocyclic Plasmin Inhibitor Deposited 2022-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 561–810（250 aa）	Mutation：S760A	GGI (5S,8R,18S,21R)-N-{[4-(aminomethyl)phenyl]methyl}-21-[(benzenesulfonyl)amino]-3,11,20-trioxo-2,5,8,12,19-pentaazatetracyclo[21.2.2.2~5,8~.2~13,16~]hentriaconta-1(25),13,15,23,26,28-hexaene-18-carboxamide × 1 SO4 SULFATE ION × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.7；293 K；14% PEG 4000, 90-140 mM Ammonium sulfate, 100 mM MES	Resolution 1.47 Å R-free 0.189
8F7V Macrocyclic plasmin inhibitor Deposited 2022-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 561–810（250 aa）	Not recorded	EUA (6S,9R,19S,22R)-N-{[4-(aminomethyl)phenyl]methyl}-22-[(benzenesulfonyl)amino]-3,12,21-trioxo-2,6,9,13,20-pentaazatetracyclo[22.2.2.2~6,9~.2~14,17~]dotriaconta-1(26),14,16,24,27,29-hexaene-19-carboxamide × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES	Resolution 1.65 Å R-free 0.187
8F7V Macrocyclic plasmin inhibitor Deposited 2022-11-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 561–810（250 aa）	Not recorded	EUA (6S,9R,19S,22R)-N-{[4-(aminomethyl)phenyl]methyl}-22-[(benzenesulfonyl)amino]-3,12,21-trioxo-2,6,9,13,20-pentaazatetracyclo[22.2.2.2~6,9~.2~14,17~]dotriaconta-1(26),14,16,24,27,29-hexaene-19-carboxamide × 1 SO4 SULFATE ION × 6 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；13-18% PEG 4000, 150 mM Ammonium sulfate, 100 mM MES	Resolution 1.65 Å R-free 0.187
8UQ6 Human Plasminogen bound to streptococcal surface enolase Deposited 2023-10-23	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–810（791 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255
9AZK Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin Deposited 2024-03-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 561–810（250 aa） Fragment：serine protease domain (UNP residues 561-810)	Not recorded	A1AHR (1r,4S)-4-(aminomethyl)-N-[(24S)-5-methyl-8,11,16,23-tetraoxo-7,10,15,22-tetraazatetracyclo[24.2.2.2~18,21~.1~2,6~]tritriaconta-1(28),2(33),3,5,18,20,26,29,31-nonaen-24-yl]cyclohexane-1-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1 M Tris-HCl, 0.2 M ammonium phosphate monobasic	Resolution 2.10 Å R-free 0.255

46 other PDB entries and 73 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PLMN_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 564–810 Author chain B； PDBConstruct 1–247； UniProt 564–810 Author chain C； PDBConstruct 1–247； UniProt 564–810 Author chain D； PDBConstruct 1–247； UniProt 564–810

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1ddj
Deposition date deposition_date	1999-11-10
Structure title title	CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN
Keywords keywords	PLASMINOGEN, CATALYTIC DOMAIN, BLOOD CLOTTING; BLOOD CLOTTING
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	43.51 Å
Radius of gyration Rg (electron density) rg_electron	43.81 Å
Forward intensity I(0) i0	175871000.00
Molecular weight molecular_weight	108200.0 kDa
Excluded volume excluded_volume	135360 Å³
Envelope volume envelope_volume	191580 Å³
Hydration-shell volume shell_volume	37701 Å³
Envelope diameter envelope_diameter	148.6 Å
Shell Rg shell_rg	46.78 Å
Envelope Rg envelope_rg	42.25 Å
Shape Rg shape_rg	43.82 Å
Total Rg total_rg	43.91 Å
Total atoms total_atoms	7600
Residues n_residues	988
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	149.2 Å
Rg (real space) rg_real	43.69 Å
Rg uncertainty (real space) rg_real_error	1.78 Å
I(0) (real space) i0_real	1.7590e+08
I(0) uncertainty (real space) i0_real_error	3.6260e+06
Rg (reciprocal space) rg_reciprocal	43.51 Å
I(0) (reciprocal space) i0_reciprocal	175800000.0000
Solution quality estimate total_estimate	0.7039
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	62.1 Å
Skewness Skewness skewness	0.290
Kurtosis Kurtosis kurtosis	-0.398
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13810000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.245; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.759; Smooth: 0.652

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1ddja_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1ddjb_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1ddjc_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d1ddjd_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (8 domains)

Domain ID domain_id	1ddjA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjC01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjC02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjD01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	1ddjD02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

▶

8. Citations (2)

▶

Unit-cell length a length_a	90.490 Å
Unit-cell length b length_b	46.160 Å
Unit-cell length c length_c	126.650 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1940
R_work r_work	0.1940
R_free r_free	0.2670

Description description	PLASMINOGEN
Molecular weight formula_weight	27080.1 kDa
EC 编号 ec_number	3.4.21.7
Mutation mutation	S741A
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	8341

CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN

1. Protein Identity and Related Structures Protein Identity & Related Structures

PLASMINOGEN

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	741

fit	/app/data/saxs_computation/dd/1ddj/1ddj.fit
pddf	/app/data/pr_computation/dd/1ddj/1ddj.pr.out
profile	/app/data/saxs_computation/dd/1ddj/1ddj.dat