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)

Method: X-RAY DIFFRACTION D_max: 95.7 Å Quality: GOOD

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

Plasminogen Activator Inhibitor-1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 24–402	Mutation：N150H-K154T-Q301P-Q319L-M354I	VHH-2g-42 × 1 VHH-2w-64 × 1	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

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 6GWP	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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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
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 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 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 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 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 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
7AQF Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) Deposited 2020-10-21	Different mutation/modification Different oligomeric state 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	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
7AQF Crystal Structure of Small Molecule Inhibitor TM5484 Bound to Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) Deposited 2020-10-21	Different mutation/modification Different oligomeric state 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	No recorded non-water small molecule	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
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 ligand/ion 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 55 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

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6gwp
Deposition date deposition_date	2018-06-25
Structure title title	Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)
Keywords keywords	;plasminogen activator inhibitor-1, PAI-1, PAI-1-stab, serpin, protease inhibitor, serine protease inhibitor, nanobody, antibody fragment, protein complex, hydrolase ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.39 Å
Radius of gyration Rg (electron density) rg_electron	29.48 Å
Forward intensity I(0) i0	71062500.00
Molecular weight molecular_weight	66514.0 kDa
Excluded volume excluded_volume	83300 Å³
Envelope volume envelope_volume	106370 Å³
Hydration-shell volume shell_volume	30853 Å³
Envelope diameter envelope_diameter	100.2 Å
Shell Rg shell_rg	35.86 Å
Envelope Rg envelope_rg	29.40 Å
Shape Rg shape_rg	29.48 Å
Total Rg total_rg	30.11 Å
Total atoms total_atoms	4686
Residues n_residues	604
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	95.7 Å
Rg (real space) rg_real	30.38 Å
Rg uncertainty (real space) rg_real_error	0.75 Å
I(0) (real space) i0_real	7.1060e+07
I(0) uncertainty (real space) i0_real_error	1.1210e+06
Rg (reciprocal space) rg_reciprocal	30.39 Å
I(0) (reciprocal space) i0_reciprocal	71060000.0000
Solution quality estimate total_estimate	0.8301
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.4 Å
Skewness Skewness skewness	0.220
Kurtosis Kurtosis kurtosis	-0.734
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11310000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.942; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Plasminogen Activator Inhibitor-1
Molecular weight formula_weight	42751.0 kDa
Mutation mutation	N150H-K154T-Q301P-Q319L-M354I
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4750

VHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFKIDDKGMAPALRHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISHLLGTGAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTPDGHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRPFQADFTSLSDQEPLHVALALQKVKIEVNESGTVASSSTAVIVSARMAPEEIIIDRPFLFVVRHNPTGTVLFMGQVMEP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	VHH-2g-42
Molecular weight formula_weight	12752.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

QVQLVESGGGLVQPGGRLRLSCAASGFTFRTYAMQWYRQSPGTERELVAAISNIGGVTDYGDSVKGRFTISRDNAKTTVYLEMNSLKPEDTATYYCSAVRLPQRYWGRGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
通用名 common_name	alpaca
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 polymer

Description description	VHH-2w-64
Molecular weight formula_weight	13087.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

QVQLVESGGGLVQAGGSLRLSCAASGFTFDDYSIAWFRQAPGKEREGVSCISSSDGSAYYADSVKGRFTISSDNAKNTVYLQMNSLKPEDTAVYYCAAVWARVCRNPYDYWGQGTQVTVSS

来源 Source

来源生物 organism	Vicugna pacos
通用名 common_name	alpaca
NCBI Class编号 ncbi_taxonomy_id	30538
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d6gwpa_
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.1 — Serpins
Superfamily Superfamily superfamily	e.1.1 — Serpins
Family Family family	e.1.1.1 — Serpins

Domain ID domain_id	d6gwpb_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d6gwpc_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (2 domains)

Domain ID domain_id	6gwpA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	497 — Antithrombin; Chain I, domain 2
Homologous superfamily homologous superfamily	10 — Antithrombin, subunit I, domain 2

Domain ID domain_id	6gwpA02
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	39 — Alpha-1-antitrypsin; domain 1
Homologous superfamily homologous superfamily	10 — Alpha-1-antitrypsin, domain 1

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8. Citations (1)

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Unit-cell length a length_a	43.681 Å
Unit-cell length b length_b	70.797 Å
Unit-cell length c length_c	98.513 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.48 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	97.674 Å
R factor r_factor	0.2041
R_work r_work	0.2029
R_free r_free	0.2250

fit	/app/data/saxs_computation/gw/6gwp/6gwp.fit
pddf	/app/data/pr_computation/gw/6gwp/6gwp.pr.out
profile	/app/data/saxs_computation/gw/6gwp/6gwp.dat

Crystal Structure of Stabilized Active Plasminogen Activator Inhibitor-1 (PAI-1-stab) in Complex with Two Inhibitory Nanobodies (VHH-2g-42, VHH-2w-64)

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

Plasminogen Activator Inhibitor-1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)