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7aqf

Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab)

Method: X-RAY DIFFRACTION Dmax: 99.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Plasminogen activator inhibitor 1

Homo sapiens

UniProt P05121

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 24–402 Not recorded RV2 5-Chloro-2-[[2-[3-(furan-3-yl)anilino]-2-oxoacetyl]amino]benzoic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；0.2 M TRISODIUM CITRATE, 10% w/v PEG 3350 Resolution 1.77 Å R-free 0.213
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 24–402 Not recorded No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.3；293 K；0.2 M TRISODIUM CITRATE, 10% w/v PEG 3350 Resolution 1.77 Å R-free 0.213

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 7AQF Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A7C HUMAN PLASMINOGEN ACTIVATOR INHIBITOR TYPE-1 IN COMPLEX WITH A PENTAPEPTIDE Deposited 1998-03-12 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–402（379 aa）
Mutation：A335E NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；pH 4.6
Resolution 1.95 Å R-free 0.210
1B3K Plasminogen activator inhibitor-1 Deposited 1998-12-11 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, 0.25 M NA CL AND 10 MM CACODYLATE PH 6.8 AT ROOM TEMPERATURE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.99 Å R-free 0.292
1B3K Plasminogen activator inhibitor-1 Deposited 1998-12-11 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, 0.25 M NA CL AND 10 MM CACODYLATE PH 6.8 AT ROOM TEMPERATURE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.99 Å R-free 0.292
1B3K Plasminogen activator inhibitor-1 Deposited 1998-12-11 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, 0.25 M NA CL AND 10 MM CACODYLATE PH 6.8 AT ROOM TEMPERATURE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.99 Å R-free 0.292
1B3K Plasminogen activator inhibitor-1 Deposited 1998-12-11 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；293 K；CRYSTALS WERE PRODUCED BY THE HANGING DROP METHOD EQUILIBRATING PURIFIED PROTEIN AT 5MG/ML IN 10 MM NA CACODYLATE, PH 6.8, O.25 M NACL, 1 MM EDTA AGAINST 27-32% SATURATED AMMONIUM SULPHATE, 0.25 M NA CL AND 10 MM CACODYLATE PH 6.8 AT ROOM TEMPERATURE, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.99 Å R-free 0.292
1C5G PLASMINOGEN ACTIVATOR INHIBITOR-1 Deposited 1999-12-07 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–402（402 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.60 Å
1DB2 CRYSTAL STRUCTURE OF NATIVE PLASMINOGEN ACTIVATOR INHIBITOR-1 Deposited 1999-11-02 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 26–402（377 aa）
Chain B 26–402（377 aa）
Mutation：N150H, K154T, Q301P, Q319L, M354I Mutation：N150H, K154T, Q301P, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；277 K；sodium chloride, sodium/potassium phosphate, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.70 Å R-free 0.299
1DVM ACTIVE FORM OF HUMAN PAI-1 Deposited 2000-01-21 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 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；NaCl, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.40 Å R-free 0.292
1DVM ACTIVE FORM OF HUMAN PAI-1 Deposited 2000-01-21 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 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；NaCl, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.40 Å R-free 0.292
1DVM ACTIVE FORM OF HUMAN PAI-1 Deposited 2000-01-21 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 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；NaCl, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.40 Å R-free 0.292
1DVM ACTIVE FORM OF HUMAN PAI-1 Deposited 2000-01-21 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 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；NaCl, MES, pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.K
Resolution 2.40 Å R-free 0.292
1DVN LATENT FORM OF PLASMINOGEN ACTIVATOR INHIBITOR-1 (PAI-1) Deposited 2000-01-21 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.9；293 K；PEG1000, MPD, MgSO4, Tris, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.10 Å R-free 0.289
1LJ5 1.8A Resolution Structure of Latent Plasminogen Activator Inhibitor-1(PAI-1) Deposited 2002-04-19 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–402（379 aa）
Not recorded DMS DIMETHYL SULFOXIDE × 4 ACY ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；PEG 4000, sodium acetate trihydrate, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 1.80 Å R-free 0.241
1OC0 plasminogen activator inhibitor-1 complex with somatomedin B domain of vitronectin Deposited 2003-02-03 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 24–402（379 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.4；10MM NAOAC, 50MM NACL, 2-9% PEG12000,25% PEG400, 50MM HEPES, PH 7.4
Resolution 2.28 Å R-free 0.252
3CVM High resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form Deposited 2008-04-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–402（382 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.02 Å R-free 0.282
3CVM High resolution structure of a stable Plasminogen activator inhibitor type-1 in its protease cleaved form Deposited 2008-04-18 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–402（382 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；0.1M Tris, 4.5M Ammonium Acetate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.02 Å R-free 0.282
3EOX High quality structure of cleaved PAI-1-stab Deposited 2008-09-29 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–402（379 aa） Fragment：PAI-1
Mutation：N150H, K154T, Q301P, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.5M lithium sulphate monohydrate, 15% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.61 Å R-free 0.256
3PB1 Crystal Structure of a Michaelis Complex between Plasminogen Activator Inhibitor-1 and Urokinase-type Plasminogen Activator Deposited 2010-10-20 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 I 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；1.4M ammonium sulfate, 0.1M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.272
3Q02 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 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 24–402（379 aa）
Mutation：W175F CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.238
3Q02 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 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 24–402（379 aa）
Mutation：W175F CL CHLORIDE ION × 1 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.238
3Q02 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–402（379 aa）
Chain B 24–402（379 aa）
Mutation：W175F Mutation：W175F CL CHLORIDE ION × 2 ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.238
3Q03 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 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 24–402（379 aa）
Mutation：W175F ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.64 Å R-free 0.225
3Q03 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 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 24–402（379 aa）
Mutation：W175F ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.64 Å R-free 0.225
3Q03 Crystal structure of plasminogen activator inhibitor-1 in a metastable active conformation. Deposited 2010-12-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 24–402（379 aa）
Chain B 24–402（379 aa）
Mutation：W175F Mutation：W175F ZN ZINC ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.1；293 K；1.7 - 3.0 M NaCl, 5 mM Mes pH 6.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.64 Å R-free 0.225
3R4L Human very long half life Plasminogen Activator Inhibitor type-1 Deposited 2011-03-17 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 24–402（379 aa） Fragment：UNP Residues 24-402
Mutation：Q197C, G355C NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.025M NACL, 27% TERT-BUTANOL, 0.050M TRIS-HCL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 2.70 Å R-free 0.282
3UT3 A novel PAI-I inhibitor and its structural mechanism Deposited 2011-11-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–402（375 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；293 K；ammonium sulfate, pH 6.1, vapor diffusion, temperature 293K
Resolution 2.42 Å R-free 0.245
3UT3 A novel PAI-I inhibitor and its structural mechanism Deposited 2011-11-25 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 28–402（375 aa）
Mutation：N150H, K154T, Q319L, M354I EMJ 2,5-dihydroxy-3-undecylcyclohexa-2,5-diene-1,4-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；293 K；ammonium sulfate, pH 6.1, vapor diffusion, temperature 293K
Resolution 2.42 Å R-free 0.245
3UT3 A novel PAI-I inhibitor and its structural mechanism Deposited 2011-11-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–402（375 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；293 K；ammonium sulfate, pH 6.1, vapor diffusion, temperature 293K
Resolution 2.42 Å R-free 0.245
3UT3 A novel PAI-I inhibitor and its structural mechanism Deposited 2011-11-25 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 28–402（375 aa）
Mutation：N150H, K154T, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6.1；293 K；ammonium sulfate, pH 6.1, vapor diffusion, temperature 293K
Resolution 2.42 Å R-free 0.245
4AQH Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976 Deposited 2012-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 24–402（379 aa）
Not recorded TB7 TERT-BUTYL 3-[(4-OXO-3H-PYRIDO[2,3-D]PYRIMIDIN-2-YL)AMINO]AZETIDINE-1-CARBOXYLATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8
Resolution 2.40 Å R-free 0.181
4AQH Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976 Deposited 2012-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–402（379 aa）
Not recorded TB7 TERT-BUTYL 3-[(4-OXO-3H-PYRIDO[2,3-D]PYRIMIDIN-2-YL)AMINO]AZETIDINE-1-CARBOXYLATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8
Resolution 2.40 Å R-free 0.181
4AQH Plasminogen activator inhibitor type-1 in complex with the inhibitor AZ3976 Deposited 2012-04-17 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 24–402（379 aa）
Not recorded TB7 TERT-BUTYL 3-[(4-OXO-3H-PYRIDO[2,3-D]PYRIMIDIN-2-YL)AMINO]AZETIDINE-1-CARBOXYLATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；PAI-1 WAS CONCENTRATED TO ABOUT 4 G/L IN A BUFFER CONTAINING 10 MM SODIUM ACETATE PH 5.6, 150 MM SODIUM CHLORIDE AND 1 MM EDTA. AZ3976 WAS DISSOLVED IN DEUTERATED DMSO AND ADDED TO THE PROTEIN SAMPLE TO A FINAL CONCENTRATION OF 0.3 MM. CRYSTALS WERE OBTAINED BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE: 2.5 UL PROTEIN SAMPLE WAS MIXED WITH 1 UL OF A WELL SOLUTION CONTAINING 2.0 M SODIUM CHLORIDE, 100 MM BIS-TRIS PH 6.8
Resolution 2.40 Å R-free 0.181
4G8O Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded SO4 SULFATE ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.71 Å R-free 0.268
4G8O Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.71 Å R-free 0.268
4G8O Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.71 Å R-free 0.268
4G8O Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded SO4 SULFATE ION × 2 96P (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.71 Å R-free 0.268
4G8R Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.19 Å R-free 0.215
4G8R Crystal Structure of a novel small molecule inactivator bound to plasminogen activator inhibitor-1 Deposited 2012-07-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 28–402（375 aa） Fragment：UNP residues 28-402
Not recorded SO4 SULFATE ION × 1 96P (2S)-3-({[3-(trifluoromethyl)phenoxy]carbonyl}amino)propane-1,2-diyl bis(3,4,5-trihydroxybenzoate) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.99 - 1.54 M ammonium sulfate, 200 mM NaCl and 100 mM Na Cacodylate pH 6.5 - 6.8., VAPOR DIFFUSION, temperature 298.0K
Resolution 2.19 Å R-free 0.215
4IC0 Crystal Structure of PAI-1 in Complex with Gallate Deposited 2012-12-09 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 24–402（379 aa）
Mutation：N150H, K154T, D158Q, Q319L, M354I GDE 3,4,5-trihydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.32 Å R-free 0.258
4IC0 Crystal Structure of PAI-1 in Complex with Gallate Deposited 2012-12-09 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 24–402（379 aa）
Mutation：N150H, K154T, D158Q, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.32 Å R-free 0.258
4IC0 Crystal Structure of PAI-1 in Complex with Gallate Deposited 2012-12-09 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 24–402（379 aa）
Mutation：N150H, K154T, D158Q, Q319L, M354I GDE 3,4,5-trihydroxybenzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.32 Å R-free 0.258
4IC0 Crystal Structure of PAI-1 in Complex with Gallate Deposited 2012-12-09 Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 24–402（379 aa）
Mutation：N150H, K154T, D158Q, Q319L, M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.1；293 K；ammonium sulfate, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.32 Å R-free 0.258
5BRR Michaelis complex of tPA-S195A:PAI-1 Deposited 2015-06-01 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 I 24–402（379 aa）
Mutation：N150H, K154T, Q319L, M354I GOL GLYCEROL × 4 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；298.15 K；8% PEG 6000, 0.1 M Tris-HCl
Resolution 3.16 Å R-free 0.276
5ZLZ Structure of tPA and PAI-1 Deposited 2018-03-31 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 I 29–402（374 aa）
Mutation：N173H, K177T, Q342L, M377I GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；4-8% PEG 3350, 20 mM bis-Tris-HCl pH 7.0
Resolution 3.58 Å R-free 0.312
6GWN Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64) Deposited 2018-06-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–402（379 aa）
Mutation：W175F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277.15 K；0.1 M Bis-Tris, 10 % w/v PEG 3350
Resolution 2.03 Å R-free 0.250
6GWP Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64) Deposited 2018-06-25 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–402（379 aa）
Mutation：N150H-K154T-Q301P-Q319L-M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, 17 % w/v PEG 3350, 3 % v/v methanol
Resolution 2.28 Å R-free 0.225
6GWQ Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with an Inhibitory Nanobody (VHH-2g-42) Deposited 2018-06-25 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 24–402（379 aa）
Mutation：N150H-K154T-Q301P-Q319L-M354I No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293.15 K；1 M succinic acid, 0.1 M HEPES, 1 % w/v PEG 2000
Resolution 2.32 Å R-free 0.230
6I8S Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1 Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–402（379 aa）
Mutation：YES [N150H, K154T, Q319L, M354I,] No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL
Resolution 2.90 Å R-free 0.243
6I8S Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1 Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 24–402（379 aa）
Mutation：YES [N150H, K154T, Q319L, M354I,] No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL
Resolution 2.90 Å R-free 0.243
6I8S Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1 Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 24–402（379 aa）
Mutation：YES [N150H, K154T, Q319L, M354I,] No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL
Resolution 2.90 Å R-free 0.243
6I8S Discovery and characterisation of an antibody that selectively modulates the inhibitory activity of plasminogen activator inhibitor-1 Deposited 2018-11-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 24–402（379 aa）
Mutation：YES [N150H, K154T, Q319L, M354I,] No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；15 MM AMMONIUM ACETATE PH 7.4, 8-10 % PEG 8000, 0.2 M LICL AND 20 % ETHYLENE GLYCOL
Resolution 2.90 Å R-free 0.243
6ZRV Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) in Complex with an Inhibitory Nanobody (VHH-s-a93, Nb93) Deposited 2020-07-15 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 24–402（379 aa）
Mutation：W175F No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293 K；1 M DIAMMONIUM PHOSPHATE, O.1 M TRISODIUM CITRATE, 0.2 M SODIUM CHLORIDE
Resolution 1.88 Å R-free 0.233
7AQG Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-W175F) Deposited 2020-10-21 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 24–402（379 aa）
Mutation：W175F RV2 5-Chloro-2-[[2-[3-(furan-3-yl)anilino]-2-oxoacetyl]amino]benzoic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1 M BIS-TRIS, 10% w/v PEG 3350
Resolution 2.27 Å R-free 0.268
9PAI CLEAVED SUBSTRATE VARIANT OF PLASMINOGEN ACTIVATOR INHIBITOR-1 Deposited 1999-03-11 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 24–359（336 aa）
Chain B 360–402（43 aa）
Mutation：A335P No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；19% (W/V) PEG 4000, 100 MM TRIS PH 8.5
Resolution 2.70 Å R-free 0.295

28 other PDB entries and 54 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAI1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–379； UniProt 24–402 Author chain B； PDBConstruct 1–379； UniProt 24–402

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 7aqf

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7aqf
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7aqf
Deposition date deposition_date2020-10-21
Structure title titleCrystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab)
Keywords keywords;plasminogen activator inhibitor-1, PAI-1, PAI-1-stab, serpin, protease inhibitor, serine protease inhibitor, small molecule inhibitor, HYDROLASE ;; HYDROLASE
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_guinier29.92 Å
Radius of gyration Rg (electron density) rg_electron29.08 Å
Forward intensity I(0) i0100585000.00
Molecular weight molecular_weight81819.0 kDa
Excluded volume excluded_volume103400 ų
Envelope volume envelope_volume125160 ų
Hydration-shell volume shell_volume35870 ų
Envelope diameter envelope_diameter103.4 Å
Shell Rg shell_rg36.31 Å
Envelope Rg envelope_rg29.11 Å
Shape Rg shape_rg29.08 Å
Total Rg total_rg29.75 Å
Total atoms total_atoms5785
Residues n_residues736
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 dmax99.4 Å
Rg (real space) rg_real29.90 Å
Rg uncertainty (real space) rg_real_error0.76 Å
I(0) (real space) i0_real1.0060e+08
I(0) uncertainty (real space) i0_real_error1.4870e+06
Rg (reciprocal space) rg_reciprocal29.91 Å
I(0) (reciprocal space) i0_reciprocal100600000.0000
Solution quality estimate total_estimate0.8872
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.9 Å
Skewness Skewness skewness0.322
Kurtosis Kurtosis kurtosis-0.392
Angular range angular_range— – 0.2650 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38930000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.945
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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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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7aqfa_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins
Domain ID domain_idd7aqfb_
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.1 — Serpins
Superfamily Superfamily superfamilye.1.1 — Serpins
Family Family familye.1.1.1 — Serpins
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8. Citations (1)

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9. Files and Curves (10)