6drz

Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor

Method: X-RAY DIFFRACTION Dmax: 109.3 Å Quality: REASONABLE

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

5HT2B receptor, BRIL 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 23–123 Not recorded CLR CHOLESTEROL × 1 OLA OLEIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 1 H8J (8alpha)-N-[(2S)-1-hydroxybutan-2-yl]-1,6-dimethyl-9,10-didehydroergoline-8-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM Tris/HCl pH 7.3-7.5, 40-100 mM MgCl2, 30% v/v PEG400 Resolution 3.10 Å R-free 0.263

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 214–314; UniProt 23–123

5HT2B receptor, BRIL chimera

Homo sapiens

UniProt P41595

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 36–248 Chain A; UniProt 313–404 Not recorded CLR CHOLESTEROL × 1 OLA OLEIC ACID × 1 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1 PEG DI(HYDROXYETHYL)ETHER × 1 PO4 PHOSPHATE ION × 1 H8J (8alpha)-N-[(2S)-1-hydroxybutan-2-yl]-1,6-dimethyl-9,10-didehydroergoline-8-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM Tris/HCl pH 7.3-7.5, 40-100 mM MgCl2, 30% v/v PEG400 Resolution 3.10 Å R-free 0.263

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.

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 5HT2B_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–213; UniProt 36–248 Author chain A; PDBConstruct 320–411; UniProt 313–404

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 6drz

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id6drz
Deposition date deposition_date2018-06-13
Structure title titleStructural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
Keywords keywordsGPCR, 5HT2B, Setotonin receptor, Methysergide, 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_guinier28.97
Radius of gyration Rg (electron density) rg_electron28.09
Forward intensity I(0) i023102500.00
Molecular weight molecular_weight40991.0 kDa
Excluded volume excluded_volume53015 ų
Envelope volume envelope_volume65279 ų
Hydration-shell volume shell_volume22362 ų
Envelope diameter envelope_diameter115.6
Shell Rg shell_rg30.74
Envelope Rg envelope_rg28.71
Shape Rg shape_rg28.11
Total Rg total_rg28.34
Total atoms total_atoms2898
Residues n_residues388
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 dmax109.3
Rg (real space) rg_real29.45
Rg uncertainty (real space) rg_real_error1.44
I(0) (real space) i0_real2.3100e+07
I(0) uncertainty (real space) i0_real_error3.5370e+05
Rg (reciprocal space) rg_reciprocal29.24
I(0) (reciprocal space) i0_reciprocal23100000.0000
Solution quality estimate total_estimate0.7362
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.9
Skewness Skewness skewness0.718
Kurtosis Kurtosis kurtosis0.026
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3155000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.476; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.187; Smooth: 0.953

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

8. Citations (1)

9. Files and Curves (10)