5nj6

Crystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in ternary complex with Fab3949 and AZ7188 at 4.0 angstrom resolution

Method: X-RAY DIFFRACTION Dmax: 164.6 Å Quality: REASONABLE

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

Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2

Homo sapiens

UniProt P0ABE7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 23–127 Mutation:;G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A,G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A,G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A ; Fab3949 H × 1 Fab3949 L × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5.7;293 K;0.1M MES pH 5.5-6.2, 0.2M POTASSIUM / SODIUM TARTRATE, 30-35% (W/V) PEG400, 2% (W/V) 2,5-HEXANEDIOL Resolution 4.00 Å R-free 0.319

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.

714 other PDB entries and 822 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C562_ECOLX
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 217–321; UniProt 23–127

Proteinase-activated receptor 2,Soluble cytochrome b562,Proteinase-activated receptor 2

Homo sapiens

UniProt P55085

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 55–269 Chain A; UniProt 276–377 Mutation:;G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A,G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A,G89A, H108A, G157A, M166L, Y174A, V176E, N222Q, M268A, I289A, L293A ; Fab3949 H × 1 Fab3949 L × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 5.7;293 K;0.1M MES pH 5.5-6.2, 0.2M POTASSIUM / SODIUM TARTRATE, 30-35% (W/V) PEG400, 2% (W/V) 2,5-HEXANEDIOL Resolution 4.00 Å R-free 0.319

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.

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PAR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–216; UniProt 55–269 Author chain A; PDBConstruct 323–424; UniProt 276–377

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 5nj6

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nj6
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nj6
Deposition date deposition_date2017-03-28
Structure title titleCrystal structure of a thermostabilised human protease-activated receptor-2 (PAR2) in ternary complex with Fab3949 and AZ7188 at 4.0 angstrom resolution
Keywords keywordsMEMBRANE PROTEIN, GPCR, 7TM; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier43.62
Radius of gyration Rg (electron density) rg_electron44.02
Forward intensity I(0) i0120058000.00
Molecular weight molecular_weight91806.0 kDa
Excluded volume excluded_volume116070 ų
Envelope volume envelope_volume163840 ų
Hydration-shell volume shell_volume35076 ų
Envelope diameter envelope_diameter163.0
Shell Rg shell_rg40.95
Envelope Rg envelope_rg45.31
Shape Rg shape_rg43.97
Total Rg total_rg44.05
Total atoms total_atoms6467
Residues n_residues832
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 dmax164.6
Rg (real space) rg_real44.49
Rg uncertainty (real space) rg_real_error2.86
I(0) (real space) i0_real1.2010e+08
I(0) uncertainty (real space) i0_real_error2.6680e+06
Rg (reciprocal space) rg_reciprocal43.63
I(0) (reciprocal space) i0_reciprocal119900000.0000
Solution quality estimate total_estimate0.6717
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary27.4
Skewness Skewness skewness0.654
Kurtosis Kurtosis kurtosis-0.364
Angular range angular_range— – 0.1800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6868000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.285; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.103; Smooth: 0.771

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5nj6A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id5nj6H02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nj6L01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id5nj6L02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)