8t1w

Crystal structure of orphan G protein-coupled receptor 6 with bound CVN424

Method: X-RAY DIFFRACTION Dmax: 96.8 Å Quality: GOOD

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

G-protein coupled receptor 6, Soluble cytochrome b562 chimera

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 23–128 Not recorded X7T 1-{2-[4-(2,4-difluorophenoxy)piperidin-1-yl]-3-{[(3R)-oxolan-3-yl]amino}-7,8-dihydropyrido[3,4-b]pyrazin-6(5H)-yl}ethan-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;NaCH3COO, PEG 400, NaCl, PPG P40 Resolution 3.49 Å R-free 0.322

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 237–342; UniProt 23–128

G-protein coupled receptor 6, Soluble cytochrome b562 chimera

Homo sapiens

UniProt P46095

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 Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 48–256 Chain A; UniProt 270–362 Not recorded X7T 1-{2-[4-(2,4-difluorophenoxy)piperidin-1-yl]-3-{[(3R)-oxolan-3-yl]amino}-7,8-dihydropyrido[3,4-b]pyrazin-6(5H)-yl}ethan-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;NaCH3COO, PEG 400, NaCl, PPG P40 Resolution 3.49 Å R-free 0.322

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.

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GPR6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 28–236; UniProt 48–256 Author chain A; PDBConstruct 344–436; UniProt 270–362

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 8t1w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8t1w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8t1w
Deposition date deposition_date2023-06-04
Structure title titleCrystal structure of orphan G protein-coupled receptor 6 with bound CVN424
Keywords keywordsOrphan GPCR, GPR6, BRIL, CVN424, inverse agonist, LCP, synchrotron, APS, membrane protein; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.46
Radius of gyration Rg (electron density) rg_electron27.44
Forward intensity I(0) i043120600.00
Molecular weight molecular_weight34870.0 kDa
Excluded volume excluded_volume34124 ų
Envelope volume envelope_volume59243 ų
Hydration-shell volume shell_volume20776 ų
Envelope diameter envelope_diameter101.7
Shell Rg shell_rg30.42
Envelope Rg envelope_rg28.06
Shape Rg shape_rg27.39
Total Rg total_rg27.78
Total atoms total_atoms2651
Residues n_residues357
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 dmax96.8
Rg (real space) rg_real28.01
Rg uncertainty (real space) rg_real_error0.87
I(0) (real space) i0_real4.3120e+07
I(0) uncertainty (real space) i0_real_error6.7070e+05
Rg (reciprocal space) rg_reciprocal27.84
I(0) (reciprocal space) i0_reciprocal43120000.0000
Solution quality estimate total_estimate0.7511
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.7
Skewness Skewness skewness0.704
Kurtosis Kurtosis kurtosis-0.127
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha6665000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.542; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.437; Smooth: 0.697

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)