7xyd

Crystal structure of TMPRSS2 in complex with Nafamostat

Method: X-RAY DIFFRACTION D_max: 107.3 Å Quality: GOOD

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

Transmembrane protease serine 2 catalytic chain

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 109–254 Chain C； UniProt 256–492	Mutation：Residues 250-255 SSRQSR were mutated to DDDDK	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；0.1M acetic acid/sodium acetate, pH 4.0, 20% w/v PEG 4000	Resolution 2.58 Å R-free 0.248
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 109–254 Chain D； UniProt 256–492	Mutation：Residues 250-255 SSRQSR were mutated to DDDDK	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4；293 K；0.1M acetic acid/sodium acetate, pH 4.0, 20% w/v PEG 4000	Resolution 2.58 Å R-free 0.248

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 7XYD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7MEQ Crystal structure of human TMPRSS2 in complex with Nafamostat Deposited 2021-04-07	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 109–492（384 aa）	Not recorded	GBS 4-carbamimidamidobenzoic acid × 1 UNX UNKNOWN LIGAND × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；30.0% (w/v) Jeffamine ED-2001 7.0, 0.1 M HEPES pH7.0	Resolution 1.95 Å R-free 0.225
7Y0E Crystal structure of TMPRSS2 in complex with Camostat Deposited 2022-06-04	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 109–254（146 aa） Chain C 256–492（237 aa）	Mutation：Residues 250-255 SSRQSR were replaced with DDDDK.	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 5.0, 16% w/v PEG 8000	Resolution 2.39 Å R-free 0.239
7Y0E Crystal structure of TMPRSS2 in complex with Camostat Deposited 2022-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：Residues 250-255 SSRQSR were replaced with DDDDK.	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 5.0, 16% w/v PEG 8000	Resolution 2.39 Å R-free 0.239
7Y0F Crystal structure of TMPRSS2 in complex with UK-371804 Deposited 2022-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 109–254（146 aa） Chain C 256–492（237 aa）	Mutation：Residues 250-255 (SSRQSR) in the database have been replaced with DDDDK.	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 I9V 2-[(1-carbamimidamido-4-chloranyl-isoquinolin-7-yl)sulfonylamino]-2-methyl-propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 5.0, 16% w/v PEG 8000	Resolution 2.60 Å R-free 0.237
7Y0F Crystal structure of TMPRSS2 in complex with UK-371804 Deposited 2022-06-04	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：Residues 250-255 (SSRQSR) in the database have been replaced with DDDDK.	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1 I9V 2-[(1-carbamimidamido-4-chloranyl-isoquinolin-7-yl)sulfonylamino]-2-methyl-propanoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 5.0, 16% w/v PEG 8000	Resolution 2.60 Å R-free 0.237
8HD8 Crystal structure of TMPRSS2 in complex with 212-148 Deposited 2022-11-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 109–254（146 aa） Chain C 256–492（237 aa）	Mutation：Residues 250-255 SSRQSR were replaced with DDDDK.	CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 4.0, 20% w/v PEG 4000	Resolution 2.40 Å R-free 0.218
8HD8 Crystal structure of TMPRSS2 in complex with 212-148 Deposited 2022-11-03	Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：Residues 250-255 SSRQSR were replaced with DDDDK.	CA CALCIUM ION × 1 GBS 4-carbamimidamidobenzoic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M acetic acid/sodium acetate, pH 4.0, 20% w/v PEG 4000	Resolution 2.40 Å R-free 0.218
8JHZ Cryo-EM structure of the TcsH-TMPRSS2 complex Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 106–492（387 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4	Resolution 3.20 Å
8JI0 Cryo-EM structure of the TcsH-CROP in complex with TMPRSS2 Deposited 2023-05-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 106–492（387 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8S0L Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07 Deposited 2024-02-14	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 107–492（386 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；20 %w/v PEG 3350, 0.05 M HEPES (pH 7.0), 1 %w/v Tryptone, 0.001 %w/v NaN3	Resolution 1.80 Å R-free 0.215
8S0M Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01 Deposited 2024-02-14	Different construct 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 B 107–492（386 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.35 M NaH2PO4, 0.65 M K2HPO4	Resolution 3.55 Å R-free 0.221
8S0M Crystal structure of the HKU1 receptor binding domain in complex with TMPRSS2 and the nanobody A01 Deposited 2024-02-14	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 E 107–492（386 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.35 M NaH2PO4, 0.65 M K2HPO4	Resolution 3.55 Å R-free 0.221
8S0N Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07 Deposited 2024-02-14	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 107–492（386 aa）	Mutation：S441A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；10 %w/v PEG 3000, 0.1 M imidazole (pH 8.0), 0.2 M lithium sulfate	Resolution 2.30 Å R-free 0.246
8S0N Crystal structure of the TMPRSS2 zymogen in complex with the nanobody A07 Deposited 2024-02-14	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 C 107–492（386 aa）	Mutation：S441A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；10 %w/v PEG 3000, 0.1 M imidazole (pH 8.0), 0.2 M lithium sulfate	Resolution 2.30 Å R-free 0.246
8V04 High resolution TMPRSS2 structure following acylation by nafamostat Deposited 2023-11-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–255（108 aa） Chain B 256–492（237 aa） Fragment：Peptidase S1 domain residues 256-492	Mutation：S251D, R252D, Q253D, S254D, R255K	EDO 1,2-ETHANEDIOL × 9 UNX UNKNOWN LIGAND × 1 GBS 4-carbamimidamidobenzoic acid × 1 CIT CITRIC ACID × 1 CA CALCIUM ION × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer containing 25 mM Tris pH 8.0, 75 mM NaCl, and 2 mM CaCl2	Resolution 1.58 Å R-free 0.181
8V1F TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–255（108 aa） Fragment：SRCR domain non-catalytic chain residues 148-254 Chain B 256–492（237 aa） Fragment：Peptidase S1 domain residues 256-492	Mutation：S251D, R252D, Q253D, S254D, R255K	TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 3 UNX UNKNOWN LIGAND × 1 EDO 1,2-ETHANEDIOL × 12 7R8 6-oxidanylnaphthalene-2-carboximidamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；precipitant containing 20% PEG3350, 0.2 M dibasic ammonium citrate. Protein mixed 1uL:1uL protein:precipitant and set as 2 uL hanging drop on glass slides	Resolution 2.19 Å R-free 0.223
8V1F TMPRSS2 complexed with the noncovalent inhibitor 6-amidino-2-napthol Deposited 2023-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 148–255（108 aa） Fragment：SRCR domain non-catalytic chain residues 148-254 Chain D 256–492（237 aa） Fragment：Peptidase S1 domain residues 256-492	Mutation：S251D, R252D, Q253D, S254D, R255K	TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 UNX UNKNOWN LIGAND × 2 EDO 1,2-ETHANEDIOL × 8 7R8 6-oxidanylnaphthalene-2-carboximidamide × 1 PEG DI(HYDROXYETHYL)ETHER × 1 CIT CITRIC ACID × 2 PG4 TETRAETHYLENE GLYCOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；precipitant containing 20% PEG3350, 0.2 M dibasic ammonium citrate. Protein mixed 1uL:1uL protein:precipitant and set as 2 uL hanging drop on glass slides	Resolution 2.19 Å R-free 0.223
8VGT Structure of the HKU1 RBD bound to the human TMPRSS2 receptor Deposited 2023-12-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
8Y1D 2up-TM conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 109–492（384 aa） Chain E 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8Y1E 3up-TM conformation of HKU1-B S protein after incubation of the receptor Deposited 2024-01-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 109–492（384 aa） Chain E 109–492（384 aa） Chain F 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 51	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
8Y7X Structure of HCoV-HKU1A spike in the functionally anchored-3up conformation with 3TMPRSS2 Deposited 2024-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain x 109–492（384 aa） Chain y 109–492（384 aa） Chain z 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 23	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.09 Å
8Y7Y Local structure of HCoV-HKU1A spike in complex with TMPRSS2 and glycan Deposited 2024-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain T 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 MJJ methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8Y87 Structure of HCoV-HKU1C spike in the functionally anchored-1up conformation with 1TMPRSS2 Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 22	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
8Y88 Structure of HCoV-HKU1C spike in the functionally anchored-2up conformation with 2TMPRSS2 Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain I 109–492（384 aa） Chain T 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
8Y89 Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 2TMPRSS2 Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain G 109–492（384 aa） Chain T 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.32 Å
8Y8A Structure of HCoV-HKU1C spike in the functionally anchored-3up conformation with 3TMPRSS2 Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 109–492（384 aa） Chain H 109–492（384 aa） Chain T 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
8Y8B Local structure of HCoV-HKU1C spike in complex with TMPRSS2 and glycan Deposited 2024-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 109–492（384 aa） Chain T 109–492（384 aa）	Not recorded	MJJ methyl 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
8YOY Structure of HKU1A RBD with TMPRSS2 Deposited 2024-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–492（384 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å
8YQQ Structure of HKU1B RBD with TMPRSS2 Deposited 2024-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–492（384 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.95 Å
9E83 TMPRSS2 crystal structure following acylation by UCSF_157 Deposited 2024-11-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 148–255（108 aa） Chain B 256–492（237 aa） Fragment：Peptidase S1 domain residues 256-492	Mutation：S251D/R252D/Q253D/S254D/R255K	CIT CITRIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 VU4 4-(2-aminoethyl)benzoic acid × 1 UNX UNKNOWN LIGAND × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；291 K；3 uL hanging drop (2:1 protein:precipitant) grown over precipitant solution containing 25%PEG4000, 0.2M ammonium sulfate, and 0.1M sodium acetate pH 4.6. Protein (10 mg/mL) was in a buffer containing 25 mM Tris pH 8.0, 75 mM NaCl, and 2 mM CaCl2	Resolution 2.07 Å R-free 0.260
9IZN Crystal structure of HKU1A RBD bound to TMPRSS2 Deposited 2024-08-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–492（384 aa）	Mutation：R255Q	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2% v/v Tacsimate pH 7.0, 5% v/v 2-Propanol, 0.1 M Imidazole (pH 7.0) and 8% w/v Polyethylene glycol 3350	Resolution 2.40 Å R-free 0.261
9JCX Crystal structure of the HCoV-HKU1 RBD and TMPRSS2 Deposited 2024-08-30	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 109–254（146 aa） Chain C 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K Mutation：S441A	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M Tris pH 7.0, 0.2 M MgCl2, 10% (w/v) Polyethylene glycol 8,000	Resolution 2.75 Å R-free 0.237
9JD0 Crystal structure of TMPRSS2 in complex with nanobody Deposited 2024-08-30	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 109–254（146 aa） Chain C 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M sodium malonate pH 6.0, 10% (w/v) Polyethylene glycol 3,350	Resolution 2.00 Å R-free 0.221
9JD0 Crystal structure of TMPRSS2 in complex with nanobody Deposited 2024-08-30	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 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MLI MALONATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；0.2 M sodium malonate pH 6.0, 10% (w/v) Polyethylene glycol 3,350	Resolution 2.00 Å R-free 0.221
9JD1 Crystal structure of TMPRSS2 in complex with Fab Deposited 2024-08-30	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 GOL GLYCEROL × 2 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；50 mM MES pH 5.6, 8.6% (w/v) Polyethylene glycol 4,000, 17.1% (v/v) Polyethylene glycol 600	Resolution 1.90 Å R-free 0.223
9K3T Cryo-EM structure of TMPRSS2 in complex with Fab fragments of 752 mAb and 2228 mAb Deposited 2024-10-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 109–492（384 aa）	Mutation：250SSRQSR255 replaced with DDDDDK	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9OPQ TMPRSS2 (S441A) bound to the HCoV-NL63 S2'region genetically fused to the HCoV-HKU1 RBD Deposited 2025-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 110–492（383 aa）	Mutation：S441A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9OPR TMPRSS2 S441A in complex with the H1H7 Fab and anti-kappa light chain nanobody Deposited 2025-05-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 110–492（383 aa）	Mutation：S441A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9U8G Crystal structure of TMPRSS2 in complex with nanobody77_10 Deposited 2025-03-26	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 109–254（146 aa） Chain B 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；100 mM HEPES/ Sodium hydroxide pH 7.0, 10% w/v PEG 6000	Resolution 2.00 Å R-free 0.230
9U8G Crystal structure of TMPRSS2 in complex with nanobody77_10 Deposited 2025-03-26	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 C 109–254（146 aa） Chain D 256–492（237 aa）	Mutation：S250D,S251D,R252D,Q253D, S254K	CA CALCIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；293 K；100 mM HEPES/ Sodium hydroxide pH 7.0, 10% w/v PEG 6000	Resolution 2.00 Å R-free 0.230
9Z3J HCoV-NL63 S2' peptide bound to TMPRSS2 S441A (complexed with the H1H7 Fab and an anti-kappa-nanobody) Deposited 2025-11-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 110–249（140 aa） Chain B 256–492（237 aa）	Mutation：S441A Mutation：S441A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å

33 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TMPS2_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–146； UniProt 109–254 Author chain B； PDBConstruct 1–146； UniProt 109–254 Author chain C； PDBConstruct 1–237； UniProt 256–492 Author chain D； PDBConstruct 1–237； UniProt 256–492

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	7xyd
Deposition date deposition_date	2022-06-01
Structure title title	Crystal structure of TMPRSS2 in complex with Nafamostat
Keywords keywords	Inhibitor, Complex, Host, Antiviral, ANTIVIRAL PROTEIN, 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	32.30 Å
Radius of gyration Rg (electron density) rg_electron	31.33 Å
Forward intensity I(0) i0	110804000.00
Molecular weight molecular_weight	80927.0 kDa
Excluded volume excluded_volume	99848 Å³
Envelope volume envelope_volume	124570 Å³
Hydration-shell volume shell_volume	33991 Å³
Envelope diameter envelope_diameter	107.9 Å
Shell Rg shell_rg	37.26 Å
Envelope Rg envelope_rg	31.41 Å
Shape Rg shape_rg	31.29 Å
Total Rg total_rg	31.94 Å
Total atoms total_atoms	5677
Residues n_residues	735
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	107.3 Å
Rg (real space) rg_real	32.42 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	1.1080e+08
I(0) uncertainty (real space) i0_real_error	1.8040e+06
Rg (reciprocal space) rg_reciprocal	32.37 Å
I(0) (reciprocal space) i0_reciprocal	110800000.0000
Solution quality estimate total_estimate	0.8863
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	0.355
Kurtosis Kurtosis kurtosis	-0.545
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	15310000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.895; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.917; Smooth: 0.916

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Transmembrane protease serine 2 catalytic chain
Molecular weight formula_weight	16054.7 kDa
Mutation mutation	Residues 250-255 SSRQSR were mutated to DDDDK
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5833

MGSKCSNSGIECDSSGTCINPSNWCDGVSHCPGGEDENRCVRLYGPNFILQVYSSQRKSWHPVCQDDWNENYGRAACRDMGYKNNFYSSQGIVDDSGSTSFMKLNTSAGNVDIYKKLYHSDACSSKAVVSLRCIACGVNLNDDDDK

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	Transmembrane protease serine 2 catalytic chain
Molecular weight formula_weight	27856.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

IVGGESALPGAWPWQVSLHVQNVHVCGGSIITPEWIVTAAHCVEKPLNNPWHWTAFAGILRQSFMFYGAGYQVEKVISHPNYDSKTKNNDIALMKLQKPLTFNDLVKPVCLPNPGMMLQPEQLCWISGWGATEEKGKTSEVLNAAKVLLIETQRCNSRYVYDNLITPAMICAGFLQGNVDSCQGDSGGPLVTSKNNIWWLIGDTSWGSGCAKAYRPGVYGNVMVFTDWIYRQMRADGEFVEHHHHHHHH

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 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	4-carbamimidamidobenzoic acid
Molecular weight formula_weight	179.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	153

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8. Citations (1)

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Unit-cell length a length_a	49.140 Å
Unit-cell length b length_b	93.203 Å
Unit-cell length c length_c	93.130 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	100.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.580 Å
Low-resolution limit resolution_low	39.810 Å
R factor r_factor	0.2142
R_work r_work	0.2114
R_free r_free	0.2477

fit	/app/data/saxs_computation/xy/7xyd/7xyd.fit
pddf	/app/data/pr_computation/xy/7xyd/7xyd.pr.out
profile	/app/data/saxs_computation/xy/7xyd/7xyd.dat

Crystal structure of TMPRSS2 in complex with Nafamostat

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

Transmembrane protease serine 2 catalytic chain

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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)