SAXSdb — 6t7p

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

Plasma kallikrein

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 391–632	Not recorded	GSH Glutathione × 1 DMS DIMETHYL SULFOXIDE × 10 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 1 MU8 (2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG10000, 200 mM Sodium phosphate (monobasic), corresponds to Nextal condition #87 from PEG series	Resolution 1.42 Å R-free 0.188

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 6T7P	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10KZ N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors Deposited 2026-01-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa）	Not recorded	A1C6O (3'R)-1'-(1-benzyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M HEPES, pH 7.0, 10-12% PEG8000	Resolution 1.78 Å R-free 0.197
10LR N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable PlasmaKallikrein Inhibitors complex with Compound 4 ((3'R)-1'-(5-amino-1-benzyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one) Deposited 2026-01-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa） Fragment：catalytic domain (UNP residues 376-638)	Mutation：C382S, C503S	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1C6Q (3'R)-1'-(5-amino-1-benzyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；0.1 M HEPES, pH 7.0, 10-12% PEG8000	Resolution 1.58 Å R-free 0.261
10MV N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors complex with Compound 15 ((3'R)-1'-(5-amino-1-phenyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one) Deposited 2026-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa） Fragment：catalytic domain (UNP residues 376-638)	Mutation：C383S, C503S	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1C6X (3'R)-1'-(5-amino-1-phenyl-1H-pyrazole-4-carbonyl)-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, pH 6.5, 24% PEG8000, 5% glycerol	Resolution 1.66 Å R-free 0.226
10MW N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors compound 25 ((3'R)-1'-{(1P)-5-amino-1-[2-(trifluoromethoxy)phenyl]-1H-pyrazole-4-carbonyl}-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one) Deposited 2026-01-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa） Fragment：catalytic domain (UNP residues 376-638)	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1C6Z (3'R)-1'-{(1P)-5-amino-1-[2-(trifluoromethoxy)phenyl]-1H-pyrazole-4-carbonyl}-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, pH 6.5, 24% PEG8000, 5% glycerol	Resolution 1.62 Å R-free 0.234
10QS N-Alkyl & N-Aryl Aminopyrazole Spirocarbamates: A Two-Pronged Lead Optimization Strategy to Identify Orally Bioavailable Plasma Kallikrein Inhibitors Compound 13 ((3'R)-1'-{5-amino-1-[(2S)-1,1,1-trifluorobutan-2-yl]-1H-pyrazole-4-carbonyl}-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one) Deposited 2026-02-02	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 376–638（263 aa） Fragment：catalytic domain (UNP residues 376-638)	Mutation：C383S. C503S	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 A1C7M (3'R)-1'-{5-amino-1-[(2S)-1,1,1-trifluorobutan-2-yl]-1H-pyrazole-4-carbonyl}-6-chloro-5-fluorospiro[[3,1]benzoxazine-4,3'-piperidin]-2(1H)-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.1 M MES, pH 6.5, 24% PEG8000, 5% glycerol	Resolution 1.73 Å R-free 0.259
2ANW Expression, crystallization and three-dimensional structure of the catalytic domain of human plasma kallikrein: Implications for structure-based design of protease inhibitors Deposited 2005-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–631（241 aa） Fragment：protease domain, enzymatically deglycosylated	Mutation：C122S	BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.5 microliter of the protein solution and 0.5 microliter of the reservoir solution (25% PEG 6000 , 0.10 M MES pH 6.5)., VAPOR DIFFUSION, HANGING DROP, temperature 290.0K	Resolution 1.85 Å R-free 0.283
2ANY Expression, Crystallization and the Three-dimensional Structure of the Catalytic Domain of Human Plasma Kallikrein: Implications for Structure-Based Design of Protease Inhibitors Deposited 2005-08-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 391–631（241 aa） Fragment：protease domain, enzymatically deglycosylated	Mutation：C122S, N21E, N72E, N113E	PO4 PHOSPHATE ION × 3 BEN BENZAMIDINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；0.5 microliter of the protein solution and 0.5 microliter of the reservoir solution (25% PEG 6000, 0.10 M MES pH 6.5) , VAPOR DIFFUSION, SITTING DROP, temperature 290.0K	Resolution 1.40 Å R-free 0.213
4OGX Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom resolution Deposited 2014-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 391–631（241 aa） Fragment：UNP residues 391-631	Mutation：N396E, N453E, N494E, C503S	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST WIZ3-4 screen condition H7, 30% MPD, 10% PEG 3350, 0.1 M imidazole pH 6.5, 0.2 M ammonium sulfate, unique puck ID QJO1-12, crystal tracking ID 242118H7 , VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.40 Å R-free 0.236
4OGY Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution Deposited 2014-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 391–631（241 aa） Fragment：UNP residues 391-631	Mutation：N396E, N453E, N494E, C503S	EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID qjo1-15, crystal tracking ID 242121d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.10 Å R-free 0.221
4OGY Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution Deposited 2014-01-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 391–631（241 aa） Fragment：UNP residues 391-631	Mutation：N396E, N453E, N494E, C503S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；FAB DX-2930 AND HUMAN PLASMA KALLIKREIN VCID 7481 AT 150 UM OR 11.7 MG/ML AGAINST INDEX screen condition D10, 20% PEG 5000 MME, 0.1 M BisTris pH 6.5 supplemented with 20% ethylene glycol as cryo-protectant, unique puck ID qjo1-15, crystal tracking ID 242121d10, VAPOR DIFFUSION, SITTING DROP, temperature 289K	Resolution 2.10 Å R-free 0.221
5F8T The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-2 Deposited 2015-12-09	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 391–629（239 aa） Fragment：UNP RESIDUES 391-629	Mutation：C122S	SO4 SULFATE ION × 4 MRZ piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；25% PEG 3350, 0.1M Hepes, pH 7.5, 20mM (NH4)2SO4	Resolution 1.75 Å R-free 0.245
5F8X The crystal structure of human plasma kallikrein in complex with its peptide inhibitor pkalin-3 Deposited 2015-12-09	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 391–629（239 aa） Fragment：UNP RESIDUES 391-629	Mutation：C122S	SO4 SULFATE ION × 8 MRZ piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；23% PEG 3350, 0.1M TRIS-HCL, PH 8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 1.55 Å R-free 0.243
5F8Z The crystal structure of human Plasma Kallikrein in complex with its peptide inhibitor pkalin-1 Deposited 2015-12-09	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 391–629（239 aa） Fragment：UNP RESIDUES 391-629	Mutation：C122S	SO4 SULFATE ION × 5 MRZ piperidine-1-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；28% PEG 3350, 0.1M TRIS-HCL PH8.5, 20MM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K	Resolution 1.50 Å R-free 0.217
5TJX Structure of human plasma kallikrein Deposited 2016-10-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa） Fragment：UNP residues 376-638	Mutation：N396E, N453E, N494E, C503S	GBT (8E)-3-amino-1-methyl-15-[(1H-pyrazol-1-yl)methyl]-7,10,11,12,24,25-hexahydro-6H,18H,23H-19,22-(metheno)pyrido[4,3-j][1,9,13,17,18]benzodioxatriazacyclohenicosin-23-one × 1 PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.2 M potassium di-hydrogen phosphate, 21 % PEG 3350	Resolution 1.41 Å R-free 0.184
6I44 Allosteric activation of human prekallikrein by apple domain disc rotation Deposited 2018-11-09	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 20–638（619 aa）	Not recorded	BEN BENZAMIDINE × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 SO4 SULFATE ION × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 4 FMT FORMIC ACID × 8 ACT ACETATE ION × 6 GLY GLYCINE × 1 SER SERINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.5；293 K；0.1M carboxylic acid, 0.1M Hepes/mops pH 7.5, 12.5%MPD, 12.5%PEG1000, 12.5%PEG3350	Resolution 1.36 Å R-free 0.196
6O1G Full length human plasma kallikrein with inhibitor Deposited 2019-02-19	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–638（638 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 7SD N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.1 M Hepes pH 7.5 0.1 M Sodium Citrate 25 % PEG 3350	Resolution 2.20 Å R-free 0.240
6O1S Structure of human plasma kallikrein protease domain with inhibitor Deposited 2019-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 376–638（263 aa）	Mutation：N377E, N434E, N475E, C383E, and C484S	PO4 PHOSPHATE ION × 1 EDO 1,2-ETHANEDIOL × 1 7SD N-[(6-amino-2,4-dimethylpyridin-3-yl)methyl]-1-({4-[(1H-pyrazol-1-yl)methyl]phenyl}methyl)-1H-pyrazole-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；24% PEG 3350, 0.2M potassium dihydrogen phosphate	Resolution 1.70 Å R-free 0.201
7N7X Crystal structure of BCX7353(ORLADEYO) in complex with human plasma kallikrein serine protease domain at 2.1 angstrom resolution Deposited 2021-06-11	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain AAA 391–626（236 aa） Fragment：Peptidase S1 domain	Mutation：N6E, N63E, N104E, C113S	0RI Orladeyo × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；25% PEG 6000, 0.1MES buffer	Resolution 2.10 Å R-free 0.259
7QOX Factor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes Deposited 2021-12-29	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 20–378（359 aa）	Not recorded	GOL GLYCEROL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 PG4 TETRAETHYLENE GLYCOL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；288 K；Morpheus screen H9 condition: 0.1M amino acids, 0.1M buffer system 3 pH8.5, 30% precipitant mix 1.	Resolution 2.32 Å R-free 0.253
7QOX Factor XI and Plasma Kallikrein apple domain structures reveals different kininogen bound complexes Deposited 2021-12-29	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 20–378（359 aa）	Not recorded	GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 2 PE4 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PG6 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；288 K；Morpheus screen H9 condition: 0.1M amino acids, 0.1M buffer system 3 pH8.5, 30% precipitant mix 1.	Resolution 2.32 Å R-free 0.253
8A3Q Human Plasma Kallekrein in complex with 14W Deposited 2022-06-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 376–638（263 aa）	Not recorded	A1J3F N-[(3-fluoranyl-4-methoxy-pyridin-2-yl)methyl]-3-(methoxymethyl)-1-[[4-[(2-oxidanylidenepyridin-1-yl)methyl]phenyl]methyl]pyrazole-4-carboxamide × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions COUNTER-DIFFUSION；pH 5.5；291 K；25% PEG 6K, 0.10 M MES, pH 6.5, 14 mg/mL protein including 20 mM Benzamidine. 1:1 ratio of protein to mother liquor at 1 + 1 microliters over a 500 microliter reservoir at 18 Celsius	Resolution 1.80 Å R-free 0.273
8FGX Cryo-EM structure of the STAR-0215 Fab in complex with active human plasma kallikrein Deposited 2022-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 20–638（619 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；Grids were prepared using a ThermoFisher Vitrobot MkIV with the chamber held at 18C and 100% relative humidity. 3.5 uL of the sample was applied to an UltrAuFoil 1.2/1.3 300 mesh grid that had been freshly glow discharged, blotted for 4 seconds, and plunge frozen in liquid ethane.	Resolution 2.62 Å
9VWT The catalytic domain of human plasma kallikrein with peptide inhibitor 070 Deposited 2025-07-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 391–627（237 aa）	Mutation：C122S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG 3350, TRIS-HCL, (NH4)2SO4	Resolution 1.77 Å R-free 0.210

21 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLKB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–242； UniProt 391–632

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6t7p
Deposition date deposition_date	2019-10-22
Structure title title	human plasmakallikrein protease domain in complex with active site directed inhibitor
Keywords keywords	S1 protease, serine protease, structure-based drug design, active site directed inhibitor, 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	18.23 Å
Radius of gyration Rg (electron density) rg_electron	17.03 Å
Forward intensity I(0) i0	14590900.00
Molecular weight molecular_weight	28419.0 kDa
Excluded volume excluded_volume	35429 Å³
Envelope volume envelope_volume	40082 Å³
Hydration-shell volume shell_volume	19029 Å³
Envelope diameter envelope_diameter	59.2 Å
Shell Rg shell_rg	23.94 Å
Envelope Rg envelope_rg	17.42 Å
Shape Rg shape_rg	16.98 Å
Total Rg total_rg	18.20 Å
Total atoms total_atoms	1981
Residues n_residues	227
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	57.9 Å
Rg (real space) rg_real	18.10 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.4590e+07
I(0) uncertainty (real space) i0_real_error	1.7650e+05
Rg (reciprocal space) rg_reciprocal	18.12 Å
I(0) (reciprocal space) i0_reciprocal	14590000.0000
Solution quality estimate total_estimate	0.8107
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.5 Å
Skewness Skewness skewness	0.115
Kurtosis Kurtosis kurtosis	-0.405
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4646000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.851; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Plasma kallikrein
Molecular weight formula_weight	27187.0 kDa
EC 编号 ec_number	3.4.21.34
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	2447

IVGGTNSSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILNLSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLNYTEFQKPICLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGKA

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

Entity 2 Entity 2 non-polymer

Description description	GLUTATHIONE
Molecular weight formula_weight	307.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DIMETHYL SULFOXIDE
Molecular weight formula_weight	78.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(2~{S},4~{R})-1-[[(3~{S})-3-azanyl-2,3-dihydro-1-benzofuran-6-yl]carbonyl]-~{N}-(3-chlorophenyl)-4-phenyl-pyrrolidine-2-carboxamide
Molecular weight formula_weight	461.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	267

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6t7pa_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (1 domains)

Domain ID domain_id	6t7pA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	57.100 Å
Unit-cell length b length_b	59.150 Å
Unit-cell length c length_c	86.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.416 Å
Low-resolution limit resolution_low	37.126 Å
R factor r_factor	0.1542
R_work r_work	0.1524
R_free r_free	0.1878

fit	/app/data/saxs_computation/t7/6t7p/6t7p.fit
pddf	/app/data/pr_computation/t7/6t7p/6t7p.pr.out
profile	/app/data/saxs_computation/t7/6t7p/6t7p.dat

human plasmakallikrein protease domain in complex with active site directed inhibitor