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9mnb

Beta1-tryptase monomer bound to inhibitory Fabs E82.AS and E104.v2

Method: ELECTRON MICROSCOPY Dmax: 205.5 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Tryptase alpha/beta-1

Homo sapiens

UniProt Q15661

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 × 6 PDB declaration: hexameric（6） Consistent with protein copy count Chain A； UniProt 31–275 Not recorded Light chain of E104.v2 Fab × 1 Heavy chain of E104v2 Fab × 1 Light chain of E82.AS Fab × 1 Heavy chain of E82.AS Fab × 1 Anti-human kappa light chain VHH × 1 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；20mM HEPES, 100mM NaCl cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.00 Å

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 9MNB Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4A6L beta-tryptase inhibitor Deposited 2011-11-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Not recorded P43 1-{3-[1-({5-[(2-fluorophenyl)ethynyl]furan-2-yl}carbonyl)piperidin-4-yl]phenyl}methanamine × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5；PEG 3000 10%, NAACETATE 100 MM PH 5, GLYCEROL 5%, NACL 1.7 M
Resolution 2.05 Å R-free 0.211
4MPU Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 SO4 SULFATE ION × 8 PG4 TETRAETHYLENE GLYCOL × 4 X2A (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, individual monocrystals equilibrated with 30% PEG1500, 0.1 M MES, pH 5.5, 0.2 M ammonium sulfate and soaked 20 hours in same solution supplemented with compound 2A, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.65 Å R-free 0.216
4MPU Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 SO4 SULFATE ION × 4 PG4 TETRAETHYLENE GLYCOL × 2 X2A (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, individual monocrystals equilibrated with 30% PEG1500, 0.1 M MES, pH 5.5, 0.2 M ammonium sulfate and soaked 20 hours in same solution supplemented with compound 2A, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.65 Å R-free 0.216
4MPV Human beta-tryptase co-crystal structure with (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded 2A4 (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide × 2 SO4 SULFATE ION × 8 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, individual monocrystals equilibrated with 30% PEG1500, 0.1 M MES, pH 5.5, 0.2 M ammonium sulfate and soaked 20 hours in same solution supplemented with compound 3A, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.31 Å R-free 0.230
4MPV Human beta-tryptase co-crystal structure with (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded 2A4 (2R,4S)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-4-hydroxy-2-(2-hydroxypropan-2-yl)-5,5-dimethyl-1,3-dioxolane-2,4-dicarboxamide × 1 SO4 SULFATE ION × 4 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, individual monocrystals equilibrated with 30% PEG1500, 0.1 M MES, pH 5.5, 0.2 M ammonium sulfate and soaked 20 hours in same solution supplemented with compound 3A, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.31 Å R-free 0.230
4MPW Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded CL CHLORIDE ION × 4 PGE TRIETHYLENE GLYCOL × 4 ACT ACETATE ION × 4 2AJ [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 4A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å R-free 0.206
4MPW Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded CL CHLORIDE ION × 2 PGE TRIETHYLENE GLYCOL × 2 ACT ACETATE ION × 2 2AJ [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzofuran-3,5-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 4A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.95 Å R-free 0.206
4MPX Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded SO4 SULFATE ION × 10 CL CHLORIDE ION × 4 PGE TRIETHYLENE GLYCOL × 4 2AV [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 6A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.233
4MPX Human beta-tryptase co-crystal structure with [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded SO4 SULFATE ION × 5 CL CHLORIDE ION × 2 PGE TRIETHYLENE GLYCOL × 2 2AV [(1,1,3,3-tetramethyldisiloxane-1,3-diyl)di-1-benzothiene-4,2-diyl]bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 6A 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.00 Å R-free 0.233
4MQA Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded SO4 SULFATE ION × 10 PG4 TETRAETHYLENE GLYCOL × 2 X00 {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 13A 30 minutes on ice prior to setup with 30% PEG3350, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.25 Å R-free 0.251
4MQA Human beta-tryptase co-crystal structure with {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) Deposited 2013-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–275（245 aa） Fragment：UNP residues 31-275
Chain B 31–275（245 aa） Fragment：UNP residues 31-275
Not recorded SO4 SULFATE ION × 5 PG4 TETRAETHYLENE GLYCOL × 1 X00 {(1,1,3,3-tetramethyldisiloxane-1,3-diyl)bis[5-(methylsulfanyl)benzene-3,1-diyl]}bis({4-[3-(aminomethyl)phenyl]piperidin-1-yl}methanone) × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound 13A 30 minutes on ice prior to setup with 30% PEG3350, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.25 Å R-free 0.251
5WI6 Human beta-1 tryptase mutant Ile99Cys Deposited 2017-07-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Mutation：I118C Mutation：I118C Mutation：I118C Mutation：I118C SO4 SULFATE ION × 7 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；292 K；ammonium sulfate, polyethylene glycol 1500
Resolution 2.72 Å R-free 0.227
6O1F Complex between soybean trypsin inhibitor beta1-tryptase and a humanized fab Deposited 2019-02-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 31–275（245 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；5% PEG 4000 0.1M lithium sulfate 0.1M Tris pH 7.5
Resolution 2.15 Å R-free 0.233
6P0P Human beta-tryptase co-crystal structure with 5-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-2-(3'-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-[1,1'-biphenyl]-3-yl)-2-hydroxy-2H-1,3,2-benzodioxaborol-2-uide Deposited 2019-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–275（275 aa）
Not recorded Y35 (3'-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}[1,1'-biphenyl]-3-yl){4-[3-(aminomethyl)phenyl]piperidin-1-yl}[3,4-di(hydroxy-kappaO)phenyl]methanonato(2-)hydroxyborate(1-) × 1 SO4 SULFATE ION × 1 PGE TRIETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound for 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate
Resolution 2.55 Å R-free 0.249
6P0P Human beta-tryptase co-crystal structure with 5-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-2-(3'-{4-[3-(aminomethyl)phenyl]piperidine-1-carbonyl}-[1,1'-biphenyl]-3-yl)-2-hydroxy-2H-1,3,2-benzodioxaborol-2-uide Deposited 2019-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–275（275 aa）
Not recorded SO4 SULFATE ION × 2 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；298 K；1.9 mg/mL protein incubated with compound for 30 minutes on ice prior to setup with 30% PEG1500, 0.1 M sodium acetate, pH 4.6, 0.2 M ammonium sulfate
Resolution 2.55 Å R-free 0.249
6VVU Anti-Tryptase fab E104.v1 bound to tryptase Deposited 2020-02-18 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 × 12 PDB declaration: dodecameric
Chain A 1–275（275 aa）
Chain B 1–275（275 aa）
Chain C 1–275（275 aa）
Chain D 1–275（275 aa）
Not recorded CA CALCIUM ION × 3 0GJ L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.5；292 K；0.1 M Tris pH 8.5, 0.2 M CaCl2, 20% PEG 4000 and 4% pentaerythritol ethoxylate
Resolution 3.00 Å R-free 0.232
8VGH CryoEM structure of tryptase in complex with wild type anti-tryptase Fab E104.v1 Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8VGI CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.2DS Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
8VGJ CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.4DS Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8VGK CryoEM structure of tryptase in complex with engineered conformationally rigid anti-tryptase Fab E104.v1.6DS Deposited 2023-12-27 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 31–275（245 aa）
Chain B 31–275（245 aa）
Chain C 31–275（245 aa）
Chain D 31–275（245 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 5.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å

14 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name TRYB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–245； UniProt 31–275

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

SAXS scattering curve SAXS Profile

SAXS profile for 9mnb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9mnb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9mnb
Deposition date deposition_date2024-12-20
Structure title titleBeta1-tryptase monomer bound to inhibitory Fabs E82.AS and E104.v2
Keywords keywordsSerine Protease, Inhibitory Antibodies, IMMUNE SYSTEM, IMMUNE SYSTEM-Hydrolase complex; IMMUNE SYSTEM/Hydrolase
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.61 Å
Radius of gyration Rg (electron density) rg_electron55.55 Å
Forward intensity I(0) i0234201000.00
Molecular weight molecular_weight124960.0 kDa
Excluded volume excluded_volume155570 ų
Envelope volume envelope_volume239540 ų
Hydration-shell volume shell_volume39979 ų
Envelope diameter envelope_diameter190.4 Å
Shell Rg shell_rg48.29 Å
Envelope Rg envelope_rg55.80 Å
Shape Rg shape_rg55.55 Å
Total Rg total_rg55.27 Å
Total atoms total_atoms8810
Residues n_residues1150
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax205.5 Å
Rg (real space) rg_real55.49 Å
Rg uncertainty (real space) rg_real_error3.19 Å
I(0) (real space) i0_real2.3420e+08
I(0) uncertainty (real space) i0_real_error5.2490e+06
Rg (reciprocal space) rg_reciprocal53.83 Å
I(0) (reciprocal space) i0_reciprocal233600000.0000
Solution quality estimate total_estimate0.6595
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.4 Å
Skewness Skewness skewness0.549
Kurtosis Kurtosis kurtosis-0.650
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9499000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.204; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.134; Smooth: 0.824
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)