SAXSdb — 4ogx

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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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 391–631	Fragment：UNP residues 391-631 Mutation：N396E, N453E, N494E, C503S	DX-2930 HEAVY CHAIN × 1 DX-2930 LIGHT CHAIN × 1 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

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 4OGX	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 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 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 oligomeric state 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 oligomeric state 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 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
4OGY Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.1 Angstrom resolution Deposited 2014-01-16	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 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 oligomeric state 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 20–638（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 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 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 oligomeric state 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
6T7P human plasmakallikrein protease domain in complex with active site directed inhibitor Deposited 2019-10-22	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 391–632（242 aa）	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
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 oligomeric state 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 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 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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 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 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 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 mutation/modification 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 1–241； UniProt 391–631

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	4ogx
Deposition date deposition_date	2014-01-16
Structure title title	Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom resolution
Keywords keywords	;FAB, ANTIBODY, KALLIKREIN, BLOOD, PLASMA, PLASMA KALLIKREIN- MEDIATED EDEMA, ACUTE HEREDITARY ANGIOEDEMA, HAE, HMWK, serpin C1-inhibitor, C1-INH, hereditary angioedema, HAW, bradykinin, Fletcher factor, Kininogenin, serine protease, edema, HYDROLASE-ANTIBODY complex ;; HYDROLASE/ANTIBODY
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	31.76 Å
Radius of gyration Rg (electron density) rg_electron	31.54 Å
Forward intensity I(0) i0	85728900.00
Molecular weight molecular_weight	72027.0 kDa
Excluded volume excluded_volume	89369 Å³
Envelope volume envelope_volume	115700 Å³
Hydration-shell volume shell_volume	32030 Å³
Envelope diameter envelope_diameter	106.7 Å
Shell Rg shell_rg	36.92 Å
Envelope Rg envelope_rg	31.39 Å
Shape Rg shape_rg	31.53 Å
Total Rg total_rg	32.02 Å
Total atoms total_atoms	5064
Residues n_residues	664
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	109.5 Å
Rg (real space) rg_real	32.02 Å
Rg uncertainty (real space) rg_real_error	1.15 Å
I(0) (real space) i0_real	8.5730e+07
I(0) uncertainty (real space) i0_real_error	1.3200e+06
Rg (reciprocal space) rg_reciprocal	31.92 Å
I(0) (reciprocal space) i0_reciprocal	85720000.0000
Solution quality estimate total_estimate	0.8498
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.6 Å
Skewness Skewness skewness	0.500
Kurtosis Kurtosis kurtosis	-0.362
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15920000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.781; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.848; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Plasma kallikrein
Molecular weight formula_weight	27144.8 kDa
EC 编号 ec_number	3.4.21.34
Mutation mutation	N396E, N453E, N494E, C503S
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	5337

IVGGTESSWGEWPWQVSLQVKLTAQRHLCGGSLIGHQWVLTAAHCFDGLPLQDVWRIYSGILELSDITKDTPFSQIKEIIIHQNYKVSEGNHDIALIKLQAPLEYTEFQKPISLPSKGDTSTIYTNCWVTGWGFSKEKGEIQNILQKVNIPLVTNEECQKRYQDYKITQRMVCAGYKEGGKDACKGDSGGPLVCKHNGMWRLVGITSWGEGCARREQPGVYTKVAEYMDWILEKTQSSDGK

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	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	DX-2930 HEAVY CHAIN
Molecular weight formula_weight	24039.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

EVQLLESGGGLVQPGGSLRLSCAASGFTFSHYIMMWVRQAPGKGLEWVSGIYSSGGITVYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAYRRIGVPRRDEFDIWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSC

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

Entity 3 Entity 3 polymer

Description description	DX-2930 LIGHT CHAIN
Molecular weight formula_weight	23446.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIQMTQSPSTLSASVGDRVTITCRASQSISSWLAWYQQKPGKAPKLLIYKASTLESGVPSRFSGSGSGTEFTLTISSLQPDDFATYYCQQYNTYWTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

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

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	270

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4ogxa_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

Domain ID domain_id	d4ogxh_
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	d4ogxl1
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.1.1.0 — automated matches

Domain ID domain_id	d4ogxl2
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.1.1.2 — C1 set domains (antibody constant domain-like)

CATH v4.4 (6 domains)

Domain ID domain_id	4ogxA01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	4ogxA02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	4ogxH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ogxH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ogxL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	4ogxL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

▶

8. Citations (1)

▶

Unit-cell length a length_a	109.610 Å
Unit-cell length b length_b	171.500 Å
Unit-cell length c length_c	42.320 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 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	41.120 Å
R factor r_factor	0.1880
R_work r_work	0.1850
R_free r_free	0.2360

fit	/app/data/saxs_computation/og/4ogx/4ogx.fit
pddf	/app/data/pr_computation/og/4ogx/4ogx.pr.out
profile	/app/data/saxs_computation/og/4ogx/4ogx.dat

Crystal structure of Fab DX-2930 in complex with human plasma kallikrein at 2.4 Angstrom resolution

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

Plasma kallikrein

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 (5)

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 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)