SAXSdb — 3gyl

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

Prostasin

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 45–305	Fragment：UNP residues 45-305, Peptidase S1 Domain of Prostasin heavy chain Mutation：C122S,N127Q,C170S	CA CALCIUM ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；20% Peg-3000, 0.2M Calcium Acetate buffered with 0.1M Tris at pH 7.0,, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.30 Å R-free 0.178

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 3GYL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3DFJ Crystal structure of human Prostasin Deposited 2008-06-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–289（245 aa） Fragment：Serine protease domain of prostasin heavy chain: Residues 45-289	Mutation：C154S, C203A	CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；298 K；100mM Bis-Tris pH 5.8, 21-26% PEG 3350, VAPOR DIFFUSION, temperature 298K	Resolution 1.45 Å R-free 0.213
3DFL Crystal structure of human Prostasin complexed to 4-guanidinobenzoic acid Deposited 2008-06-12	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 45–289（245 aa） Fragment：Serine protease domain of prostasin heavy chain: Residues 45-289	Mutation：C154S, C203A	GBS 4-carbamimidamidobenzoic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.8；298 K；100mM Bis-Tris pH 5.8, 21-26% PEG 3350, VAPOR DIFFUSION, temperature 298K	Resolution 2.00 Å R-free 0.225
3E0N The X-ray structure of Human Prostasin in complex with DFFR-chloromethyl ketone inhibitor Deposited 2008-07-31	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 45–309（265 aa） Fragment：UNP residues 45-305	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å R-free 0.202
3E0P The X-ray structure of Human Prostasin in complex with a covalent benzoxazole inhibitor Deposited 2008-07-31	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 45–305（261 aa） Fragment：UNP residues 45-305	Not recorded	B3C benzyl [(1R)-1-({(2S,4R)-2-({(1S)-5-amino-1-[(S)-1,3-benzoxazol-2-yl(hydroxy)methyl]pentyl}carbamoyl)-4-[(4-methylbenzyl)oxy]pyrrolidin-1-yl}carbonyl)-3-phenylpropyl]carbamate × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；28% PEGME-5000 buffered with 0.1M Mes, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.70 Å R-free 0.224
3E16 X-ray structure of human prostasin in complex with Benzoxazole warhead peptidomimic, lysine in P3 Deposited 2008-08-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 45–305（261 aa） Fragment：UNP residues 45-305	Not recorded	GOL GLYCEROL × 1 B4C benzyl [(1S)-5-amino-1-{[(1S)-1-({(1S)-5-amino-1-[(S)-1,3-benzoxazol-2-yl(hydroxy)methyl]pentyl}carbamoyl)-3-phenylpropyl]carbamoyl}pentyl]carbamate × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% PEG-6000 buffered with 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.229
3E1X The Crystal Structure of Apo Prostasin at 1.7 Angstroms Resolution Deposited 2008-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 45–305（261 aa） Fragment：UNP residues 45-305	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；30% Peg-6000 in 0.1M MES buffer, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.70 Å R-free 0.215
3FVF The Crystal Structure of Prostasin Complexed with Camostat at 1.6 Angstroms Resolution Deposited 2009-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 45–305（261 aa） Fragment：UNP residues 45-305, Peptidase S1 domain	Mutation：C122S,N127Q,C170S	GOL GLYCEROL × 1 1JZ 1-[4-(hydroxymethyl)phenyl]guanidine × 1 DMS DIMETHYL SULFOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；20% PEG-6000 buffered with 0.1M MES, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.192
3GYM Structure of Prostasin in Complex with Aprotinin Deposited 2009-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 45–305（261 aa） Fragment：UNP residues 45-305, Peptidase S1 domain	Mutation：C122S,N127Q,C170S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.6M potassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M sodium chloride in an imidazole buffer at pH 8.0., VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.271
3GYM Structure of Prostasin in Complex with Aprotinin Deposited 2009-04-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 45–305（261 aa） Fragment：UNP residues 45-305, Peptidase S1 domain	Mutation：C122S,N127Q,C170S	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；1.6M potassium hydrogen phosphate, 0.4M sodium dihydrogen phosphate, 0.2M sodium chloride in an imidazole buffer at pH 8.0., VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.80 Å R-free 0.271

8 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PRSS8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain B； PDBConstruct 1–261； UniProt 45–305

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	3gyl
Deposition date deposition_date	2009-04-03
Structure title title	Structure of Prostasin at 1.3 Angstroms resolution in complex with a Calcium Ion.
Keywords keywords	;PROSTASIN, ENAC, ZYMOGEN, DIVALENT CATION, CHANNEL ACTIVATING, Cell membrane, Disulfide bond, Glycoprotein, Hydrolase, Membrane, Protease, Secreted, Serine protease, Transmembrane ;; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.09 Å
Radius of gyration Rg (electron density) rg_electron	16.95 Å
Forward intensity I(0) i0	13069500.00
Molecular weight molecular_weight	26790.0 kDa
Excluded volume excluded_volume	33378 Å³
Envelope volume envelope_volume	37597 Å³
Hydration-shell volume shell_volume	18148 Å³
Envelope diameter envelope_diameter	57.9 Å
Shell Rg shell_rg	23.55 Å
Envelope Rg envelope_rg	17.31 Å
Shape Rg shape_rg	16.95 Å
Total Rg total_rg	17.95 Å
Total atoms total_atoms	1886
Residues n_residues	212
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	59.0 Å
Rg (real space) rg_real	17.95 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	1.3070e+07
I(0) uncertainty (real space) i0_real_error	1.8090e+05
Rg (reciprocal space) rg_reciprocal	17.97 Å
I(0) (reciprocal space) i0_reciprocal	13070000.0000
Solution quality estimate total_estimate	0.8031
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	23.1 Å
Skewness Skewness skewness	0.155
Kurtosis Kurtosis kurtosis	-0.373
Angular range angular_range	— – 0.4400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3806000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.815; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Prostasin
Molecular weight formula_weight	28226.6 kDa
EC 编号 ec_number	3.4.21.-
Mutation mutation	C122S,N127Q,C170S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	2347

ITGGSSAVAGQWPWQVSITYEGVHVCGGSLVSEQWVLSAAHCFPSEHHKEAYEVKLGAHQLDSYSEDAKVSTLKDIIPHPSYLQEGSQGDIALLQLSRPITFSRYIRPISLPAAQASFPNGLHCTVTGWGHVAPSVSLLTPKPLQQLEVPLISRETCNSLYNIDAKPEEPHFVQEDMVCAGYVEGGKDACQGDSGGPLSCPVEGLWYLTGIVSWGDACGARNRPGVYTLASSYASWIQSKVTELQPRVVPQTQESQPDSNL

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 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	367

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d3gylb_
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.47.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3gylB01
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	3gylB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	54.112 Å
Unit-cell length b length_b	54.039 Å
Unit-cell length c length_c	82.553 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	45.000 Å
R factor r_factor	0.1544
R_work r_work	0.1531
R_free r_free	0.1776

fit	/app/data/saxs_computation/gy/3gyl/3gyl.fit
pddf	/app/data/pr_computation/gy/3gyl/3gyl.pr.out
profile	/app/data/saxs_computation/gy/3gyl/3gyl.dat

Structure of Prostasin at 1.3 Angstroms resolution in complex with a Calcium Ion.

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

Prostasin

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