6zdr

Crystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4d

Method: X-RAY DIFFRACTION Dmax: 106.2 Å Quality: REASONABLE

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

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a

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 23–127 Not recorded QGE [3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl] ethanoate × 1 NA SODIUM ION × 1 CLR CHOLESTEROL × 3 OLA OLEIC ACID × 11 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;PEG 400; Sodium Citrate; Sodium Thiocyanate; 2,5 Hexanediol Resolution 1.92 Å R-free 0.218

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 218–322; UniProt 23–127

Adenosine receptor A2a,Soluble cytochrome b562,Adenosine receptor A2a

Homo sapiens

UniProt P29274

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 2–208 Chain A; UniProt 219–317 Not recorded QGE [3-(4-methyl-1,3-thiazol-2-yl)-4-oxidanylidene-6-propyl-chromen-7-yl] ethanoate × 1 NA SODIUM ION × 1 CLR CHOLESTEROL × 3 OLA OLEIC ACID × 11 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 4 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;PEG 400; Sodium Citrate; Sodium Thiocyanate; 2,5 Hexanediol Resolution 1.92 Å R-free 0.218

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.

185 other PDB entries and 189 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AA2AR_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–217; UniProt 2–208 Author chain A; PDBConstruct 324–422; UniProt 219–317

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 6zdr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zdr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6zdr
Deposition date deposition_date2020-06-15
Structure title titleCrystal structure of stabilized A2A adenosine receptor A2AR-StaR2-bRIL in complex with Chromone 4d
Keywords keywordsG protein-coupled receptor, membrane protein, receptor, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.43
Radius of gyration Rg (electron density) rg_electron29.53
Forward intensity I(0) i026615700.00
Molecular weight molecular_weight46654.0 kDa
Excluded volume excluded_volume61375 ų
Envelope volume envelope_volume75442 ų
Hydration-shell volume shell_volume24168 ų
Envelope diameter envelope_diameter110.7
Shell Rg shell_rg32.34
Envelope Rg envelope_rg30.07
Shape Rg shape_rg29.50
Total Rg total_rg30.00
Total atoms total_atoms3285
Residues n_residues383
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 dmax106.2
Rg (real space) rg_real30.99
Rg uncertainty (real space) rg_real_error1.31
I(0) (real space) i0_real2.6620e+07
I(0) uncertainty (real space) i0_real_error4.6520e+05
Rg (reciprocal space) rg_reciprocal30.75
I(0) (reciprocal space) i0_reciprocal26610000.0000
Solution quality estimate total_estimate0.7167
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary22.4
Skewness Skewness skewness0.657
Kurtosis Kurtosis kurtosis-0.241
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3760000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.561; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.290; Smooth: 0.341

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)