8zmf

Crystal structure of an inverse agonist antipsychotic drug derivative-bound 5-HT2C

Method: X-RAY DIFFRACTION Dmax: 89.2 Å Quality: GOOD

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

5-hydroxytryptamine receptor 2C,Soluble cytochrome b562

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 Mutation:M29W,H124I,R128L,C360N A1L10 1-[(4-fluorophenyl)methyl]-1-[(8~{S})-5-methyl-5-azaspiro[2.5]octan-8-yl]-3-[[4-(2-methylpropoxy)phenyl]methyl]urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;18-24% PEG300, 40-60 mM ammonium phosphate dibasic Resolution 3.60 Å R-free 0.285

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 233–338; UniProt 23–128

5-hydroxytryptamine receptor 2C,Soluble cytochrome b562

Homo sapiens

UniProt P28335

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 40–245 Chain A; UniProt 301–393 Mutation:M29W,H124I,R128L,C360N A1L10 1-[(4-fluorophenyl)methyl]-1-[(8~{S})-5-methyl-5-azaspiro[2.5]octan-8-yl]-3-[[4-(2-methylpropoxy)phenyl]methyl]urea × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;18-24% PEG300, 40-60 mM ammonium phosphate dibasic Resolution 3.60 Å R-free 0.285

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.

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 5HT2C_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 27–232; UniProt 40–245 Author chain A; PDBConstruct 339–431; UniProt 301–393

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 8zmf

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id8zmf
Deposition date deposition_date2024-05-23
Structure title titleCrystal structure of an inverse agonist antipsychotic drug derivative-bound 5-HT2C
Keywords keywordsclass A G protein-coupled receptor, inverse agonist, 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_guinier25.66
Radius of gyration Rg (electron density) rg_electron24.89
Forward intensity I(0) i020462300.00
Molecular weight molecular_weight38148.0 kDa
Excluded volume excluded_volume49408 ų
Envelope volume envelope_volume60454 ų
Hydration-shell volume shell_volume21913 ų
Envelope diameter envelope_diameter93.3
Shell Rg shell_rg29.82
Envelope Rg envelope_rg25.70
Shape Rg shape_rg24.87
Total Rg total_rg25.62
Total atoms total_atoms2685
Residues n_residues331
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 dmax89.2
Rg (real space) rg_real25.90
Rg uncertainty (real space) rg_real_error0.86
I(0) (real space) i0_real2.0460e+07
I(0) uncertainty (real space) i0_real_error3.0860e+05
Rg (reciprocal space) rg_reciprocal25.83
I(0) (reciprocal space) i0_reciprocal20460000.0000
Solution quality estimate total_estimate0.8406
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary23.0
Skewness Skewness skewness0.587
Kurtosis Kurtosis kurtosis-0.104
Angular range angular_range— – 0.3100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2973000.0000
Real-space data points n_real_points63
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.724; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.775; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

8. Citations (1)

9. Files and Curves (10)