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9azk

Macrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin

Method: X-RAY DIFFRACTION Dmax: 115.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Plasminogen

Homo sapiens

UniProt P00747

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 561–810 Fragment：serine protease domain (UNP residues 561-810) 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 561–810 Fragment：serine protease domain (UNP residues 561-810) 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 561–810 Fragment：serine protease domain (UNP residues 561-810) 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
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain D； UniProt 561–810 Fragment：serine protease domain (UNP residues 561-810) 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
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain E； UniProt 561–810 Fragment：serine protease domain (UNP residues 561-810) 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
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain F； UniProt 561–810 Fragment：serine protease domain (UNP residues 561-810) 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

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 9AZK 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 ligand/ion 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 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 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 mutation/modification 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 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 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 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 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 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
1DDJ CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN Deposited 1999-11-10 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 564–810（247 aa） Fragment：CATALYTIC DOMAIN
Mutation：S741A No recorded non-water small molecule 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
1DDJ CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN Deposited 1999-11-10 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 564–810（247 aa） Fragment：CATALYTIC DOMAIN
Mutation：S741A No recorded non-water small molecule 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
1DDJ CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN Deposited 1999-11-10 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 564–810（247 aa） Fragment：CATALYTIC DOMAIN
Mutation：S741A No recorded non-water small molecule 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
1DDJ CRYSTAL STRUCTURE OF HUMAN PLASMINOGEN CATALYTIC DOMAIN Deposited 1999-11-10 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 564–810（247 aa） Fragment：CATALYTIC DOMAIN
Mutation：S741A No recorded non-water small molecule 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
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 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 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 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 ligand/ion 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 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 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） 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 mutation/modification 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 mutation/modification 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 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：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 mutation/modification 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 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 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 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）
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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）
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 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 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 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 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 oligomeric state Different ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 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 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 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 ligand/ion 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

46 other PDB entries and 71 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 1–250； UniProt 561–810 Author chain B； PDBConstruct 1–250； UniProt 561–810 Author chain C； PDBConstruct 1–250； UniProt 561–810 Author chain D； PDBConstruct 1–250； UniProt 561–810 Author chain E； PDBConstruct 1–250； UniProt 561–810 Author chain F； PDBConstruct 1–250； UniProt 561–810

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

SAXS profile for 9azk

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9azk
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9azk
Deposition date deposition_date2024-03-11
Structure title titleMacrocyclic inhibitors targeting the prime site of the fibrinolytic serine protease plasmin
Keywords keywordsprotease inhibitor, fibrinolysis, HYDROLASE-INHIBITOR complex; HYDROLASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.07 Å
Radius of gyration Rg (electron density) rg_electron36.48 Å
Forward intensity I(0) i0398933000.00
Molecular weight molecular_weight163770.0 kDa
Excluded volume excluded_volume205560 ų
Envelope volume envelope_volume259360 ų
Hydration-shell volume shell_volume58438 ų
Envelope diameter envelope_diameter124.4 Å
Shell Rg shell_rg43.47 Å
Envelope Rg envelope_rg35.87 Å
Shape Rg shape_rg36.48 Å
Total Rg total_rg36.91 Å
Total atoms total_atoms11793
Residues n_residues1464
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax115.0 Å
Rg (real space) rg_real36.86 Å
Rg uncertainty (real space) rg_real_error0.66 Å
I(0) (real space) i0_real3.9890e+08
I(0) uncertainty (real space) i0_real_error6.0470e+06
Rg (reciprocal space) rg_reciprocal36.99 Å
I(0) (reciprocal space) i0_reciprocal399000000.0000
Solution quality estimate total_estimate0.8952
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.8 Å
Skewness Skewness skewness0.125
Kurtosis Kurtosis kurtosis-0.452
Angular range angular_range— – 0.2150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha128900000.0000
Real-space data points n_real_points44
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.916; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.890
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)