SAXSdb — 4mpu

▼

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

Tryptase alpha/beta-1

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 31–275 Chain B； UniProt 31–275	Fragment：UNP residues 31-275	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 31–275 Chain B； UniProt 31–275	Fragment：UNP residues 31-275	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

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 4MPU	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 ligand/ion 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
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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 1–275（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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 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 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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
9MNB Beta1-tryptase monomer bound to inhibitory Fabs E82.AS and E104.v2 Deposited 2024-12-20	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 × 6 PDB declaration: hexameric	Chain A 31–275（245 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM HEPES, 100mM NaCl cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

14 other PDB entries and 19 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TRYB1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–245； UniProt 31–275 Author chain B； 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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4mpu
Deposition date deposition_date	2013-09-13
Structure title title	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
Keywords keywords	;coferon, alpha-hydroxyketone, small molecule inhibitor, drug discovery, self-assembly, crystal catalysis, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	24.92 Å
Radius of gyration Rg (electron density) rg_electron	24.40 Å
Forward intensity I(0) i0	52577200.00
Molecular weight molecular_weight	56340.0 kDa
Excluded volume excluded_volume	70299 Å³
Envelope volume envelope_volume	82196 Å³
Hydration-shell volume shell_volume	27912 Å³
Envelope diameter envelope_diameter	83.2 Å
Shell Rg shell_rg	31.96 Å
Envelope Rg envelope_rg	24.46 Å
Shape Rg shape_rg	24.43 Å
Total Rg total_rg	25.13 Å
Total atoms total_atoms	3966
Residues n_residues	486
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

▼

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

Maximum dimension Dmax dmax	84.7 Å
Rg (real space) rg_real	24.92 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	5.2580e+07
I(0) uncertainty (real space) i0_real_error	6.8860e+05
Rg (reciprocal space) rg_reciprocal	24.92 Å
I(0) (reciprocal space) i0_reciprocal	52580000.0000
Solution quality estimate total_estimate	0.6407
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.367
Kurtosis Kurtosis kurtosis	-0.364
Angular range angular_range	— – 0.3200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17040000.0000
Real-space data points n_real_points	64
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 0.992; Sysdev: 0.338; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Tryptase alpha/beta-1
Molecular weight formula_weight	27491.4 kDa
EC 编号 ec_number	3.4.21.59
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	4793

IVGGQEAPRSKWPWQVSLRVHGPYWMHFCGGSLIHPQWVLTAAHCVGPDVKDLAALRVQLREQHLYYQDQLLPVSRIIVHPQFYTAQIGADIALLELEEPVKVSSHVHTVTLPPASETFPPGMPCWVTGWGDVDNDERLPPPFPLKQVKVPIMENHICDAKYHLGAYTGDDVRIVRDDMLCAGNTRRDSCQGDSGGPLVCKVNGTWLQAGVVSWGEGCAQPNRPGIYTRVTYYLDWIHHYVPKKP

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	Komagataella pastoris

Entity 2 Entity 2 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	;(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 ;
Molecular weight formula_weight	871.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	515

▼

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4mpua_
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	d4mpub_
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 (4 domains)

Domain ID domain_id	4mpuA01
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	4mpuA02
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	4mpuB01
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	4mpuB02
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

▶

8. Citations (1)

▶

Unit-cell length a length_a	78.157 Å
Unit-cell length b length_b	78.157 Å
Unit-cell length c length_c	165.039 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.649 Å
Low-resolution limit resolution_low	19.800 Å
R factor r_factor	0.1802
R_work r_work	0.1782
R_free r_free	0.2161

fit	/app/data/saxs_computation/mp/4mpu/4mpu.fit
pddf	/app/data/pr_computation/mp/4mpu/4mpu.pr.out
profile	/app/data/saxs_computation/mp/4mpu/4mpu.dat

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