6n48

Structure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator

Method: X-RAY DIFFRACTION Dmax: 119.2 Å Quality: GOOD

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

Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera

Homo sapiens

UniProt A0A097J809

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 2–161 Fragment:chimera of lysozyme and B2AR (UNP residues 29-234,263-348) Mutation:M1096T, M1098T, N1187E Camelid Antibody Fragment × 1 P0G 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one × 1 1WV (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1 KBY N-[(3R)-4-(4-tert-butylphenyl)-3-({2-[(4-methoxyphenyl)sulfanyl]-5-[methyl(propan-2-yl)sulfamoyl]benzene-1-carbonyl}amino)butanoyl]glycine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 8;293 K;100 mM Tris-HCl, pH 8.0, 150-200 mM lithium acetate, 43-45% PEG400 Resolution 3.20 Å R-free 0.274

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.

16 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name A0A097J809_BPT4
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 16–175; UniProt 2–161

Endolysin,Beta-2 adrenergic receptor,Beta-2 adrenergic receptor chimera

Homo sapiens

UniProt P07550

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 29–234 Chain A; UniProt 263–348 Fragment:chimera of lysozyme and B2AR (UNP residues 29-234,263-348) Mutation:M1096T, M1098T, N1187E Camelid Antibody Fragment × 1 P0G 8-[(1R)-2-{[1,1-dimethyl-2-(2-methylphenyl)ethyl]amino}-1-hydroxyethyl]-5-hydroxy-2H-1,4-benzoxazin-3(4H)-one × 1 1WV (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1 KBY N-[(3R)-4-(4-tert-butylphenyl)-3-({2-[(4-methoxyphenyl)sulfanyl]-5-[methyl(propan-2-yl)sulfamoyl]benzene-1-carbonyl}amino)butanoyl]glycine × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;pH 8;293 K;100 mM Tris-HCl, pH 8.0, 150-200 mM lithium acetate, 43-45% PEG400 Resolution 3.20 Å R-free 0.274

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.

143 other PDB entries and 145 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ADRB2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 178–383; UniProt 29–234 Author chain A; PDBConstruct 384–469; UniProt 263–348

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 6n48

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6n48
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6n48
Deposition date deposition_date2018-11-17
Structure title titleStructure of beta2 adrenergic receptor bound to BI167107, Nanobody 6B9, and a positive allosteric modulator
Keywords keywordsG protein coupled receptor, membrane protein, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.59
Radius of gyration Rg (electron density) rg_electron34.02
Forward intensity I(0) i061321300.00
Molecular weight molecular_weight65037.0 kDa
Excluded volume excluded_volume82584 ų
Envelope volume envelope_volume106720 ų
Hydration-shell volume shell_volume29146 ų
Envelope diameter envelope_diameter126.6
Shell Rg shell_rg36.33
Envelope Rg envelope_rg33.99
Shape Rg shape_rg34.00
Total Rg total_rg34.31
Total atoms total_atoms4585
Residues n_residues574
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 dmax119.2
Rg (real space) rg_real35.04
Rg uncertainty (real space) rg_real_error1.84
I(0) (real space) i0_real6.1320e+07
I(0) uncertainty (real space) i0_real_error1.1630e+06
Rg (reciprocal space) rg_reciprocal34.76
I(0) (reciprocal space) i0_reciprocal61310000.0000
Solution quality estimate total_estimate0.7713
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.9
Skewness Skewness skewness0.571
Kurtosis Kurtosis kurtosis-0.418
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8002000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.605; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.520; Smooth: 0.696

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6n48A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology530 — Lysozyme
Homologous superfamily homologous superfamily40
Domain ID domain_id6n48A02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily10 — Rhodopsin 7-helix transmembrane proteins

8. Citations (1)

9. Files and Curves (10)