3gym

Structure of Prostasin in Complex with Aprotinin

Method: X-RAY DIFFRACTION Dmax: 104.4 Å Quality: REASONABLE

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

Prostasin

Homo sapiens

UniProt Q16651

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 45–305 Fragment:UNP residues 45-305, Peptidase S1 domain Mutation:C122S,N127Q,C170S Pancreatic trypsin inhibitor × 1 (P00974) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 45–305 Fragment:UNP residues 45-305, Peptidase S1 domain Mutation:C122S,N127Q,C170S Pancreatic trypsin inhibitor × 1 (P00974) 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

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.

8 other PDB entries and 8 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 A; PDBConstruct 1–261; UniProt 45–305 Author chain B; PDBConstruct 1–261; UniProt 45–305

Pancreatic trypsin inhibitor

Bos taurus

UniProt P00974

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 36–93 Not recorded Prostasin × 1 (Q16651) 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain J; UniProt 36–93 Not recorded Prostasin × 1 (Q16651) 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

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.

123 other PDB entries and 264 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name BPT1_BOVIN
Isoform
PDB entities 2
Chains and sequence ranges Author chain I; PDBConstruct 1–58; UniProt 36–93 Author chain J; PDBConstruct 1–58; UniProt 36–93

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 3gym

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gym
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gym
Deposition date deposition_date2009-04-03
Structure title titleStructure of Prostasin in Complex with Aprotinin
Keywords keywords;Prostasin, hCAP1, channel Activating, Aprotinin, inhibition, Disulfide bond, Pharmaceutical, Protease inhibitor, Secreted, Serine protease inhibitor, Cell membrane, Glycoprotein, Hydrolase, Membrane, Protease, Serine protease, Transmembrane, Zymogen, HYDROLASE-INHIBITOR COMPLEX ;; HYDROLASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.28
Radius of gyration Rg (electron density) rg_electron29.95
Forward intensity I(0) i068596800.00
Molecular weight molecular_weight64185.0 kDa
Excluded volume excluded_volume79843 ų
Envelope volume envelope_volume100900 ų
Hydration-shell volume shell_volume29371 ų
Envelope diameter envelope_diameter111.5
Shell Rg shell_rg35.16
Envelope Rg envelope_rg30.24
Shape Rg shape_rg29.92
Total Rg total_rg30.53
Total atoms total_atoms4514
Residues n_residues520
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax104.4
Rg (real space) rg_real30.52
Rg uncertainty (real space) rg_real_error1.08
I(0) (real space) i0_real6.8600e+07
I(0) uncertainty (real space) i0_real_error1.1810e+06
Rg (reciprocal space) rg_reciprocal30.42
I(0) (reciprocal space) i0_reciprocal68590000.0000
Solution quality estimate total_estimate0.6417
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.1
Skewness Skewness skewness0.502
Kurtosis Kurtosis kurtosis-0.388
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15160000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.727; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.706; Smooth: 0.870

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3gyma_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.0 — automated matches
Domain ID domain_idd3gymb_
Class classb — All beta proteins
Fold Fold foldb.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamilyb.47.1 — Trypsin-like serine proteases
Family Family familyb.47.1.0 — automated matches
Domain ID domain_idd3gymi_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins
Domain ID domain_idd3gymj_
Class classg — Small proteins
Fold Fold foldg.8 — BPTI-like
Superfamily Superfamily superfamilyg.8.1 — BPTI-like
Family Family familyg.8.1.1 — Small Kunitz-type inhibitors & BPTI-like toxins

CATH v4.4 (6 domains)

Domain ID domain_id3gymA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3gymA02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3gymB01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3gymB02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology10 — Thrombin, subunit H
Homologous superfamily homologous superfamily10 — Trypsin-like serine proteases
Domain ID domain_id3gymI00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain
Domain ID domain_id3gymJ00
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology410 — Factor Xa Inhibitor
Homologous superfamily homologous superfamily10 — Pancreatic trypsin inhibitor Kunitz domain

8. Citations (1)

9. Files and Curves (10)