6a93

Crystal structure of 5-HT2AR in complex with risperidone

Method: X-RAY DIFFRACTION Dmax: 124.9 Å Quality: GOOD

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

5-hydroxytryptamine receptor 2A,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 23–62 Chain A; UniProt 88–128 Mutation:S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 ZN ZINC ION × 1 1PE PENTAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO Resolution 3.00 Å R-free 0.275
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 23–62 Chain B; UniProt 88–128 Mutation:S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO Resolution 3.00 Å R-free 0.275

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 821 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 200–239; UniProt 23–62 Author chain A; PDBConstruct 245–285; UniProt 88–128 Author chain B; PDBConstruct 200–239; UniProt 23–62 Author chain B; PDBConstruct 245–285; UniProt 88–128

5-hydroxytryptamine receptor 2A,Soluble cytochrome b562

Homo sapiens

UniProt P28223

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 70–265 Chain A; UniProt 313–403 Mutation:S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 ZN ZINC ION × 1 1PE PENTAETHYLENE GLYCOL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO Resolution 3.00 Å R-free 0.275
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 70–265 Chain B; UniProt 313–403 Mutation:S162K, M164W, R120I, H124I, R128G, M29W 8NU 3-[2-[4-(6-fluoranyl-1,2-benzoxazol-3-yl)piperidin-1-yl]ethyl]-2-methyl-6,7,8,9-tetrahydropyrido[1,2-a]pyrimidin-4-one × 1 CLR CHOLESTEROL × 1 PLM PALMITIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:LIPIDIC CUBIC PHASE;293 K;100 mM MES, pH 6.0-6.5, 28-31% (v/v) PEG 400, 120-200 mM Am-formate, 1-2% (v/v) DMSO Resolution 3.00 Å R-free 0.275

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.

38 other PDB entries and 44 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name 5HT2A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 4–199; UniProt 70–265 Author chain A; PDBConstruct 286–376; UniProt 313–403 Author chain B; PDBConstruct 4–199; UniProt 70–265 Author chain B; PDBConstruct 286–376; UniProt 313–403

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 6a93

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a93
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a93
Deposition date deposition_date2018-07-11
Structure title titleCrystal structure of 5-HT2AR in complex with risperidone
Keywords keywordsMEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier36.23
Radius of gyration Rg (electron density) rg_electron35.25
Forward intensity I(0) i090047500.00
Molecular weight molecular_weight83692.0 kDa
Excluded volume excluded_volume108160 ų
Envelope volume envelope_volume144290 ų
Hydration-shell volume shell_volume35787 ų
Envelope diameter envelope_diameter133.1
Shell Rg shell_rg39.72
Envelope Rg envelope_rg34.86
Shape Rg shape_rg35.23
Total Rg total_rg35.71
Total atoms total_atoms5889
Residues n_residues729
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 dmax124.9
Rg (real space) rg_real36.31
Rg uncertainty (real space) rg_real_error1.51
I(0) (real space) i0_real9.0050e+07
I(0) uncertainty (real space) i0_real_error1.8830e+06
Rg (reciprocal space) rg_reciprocal36.26
I(0) (reciprocal space) i0_reciprocal90040000.0000
Solution quality estimate total_estimate0.8636
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary48.2
Skewness Skewness skewness0.306
Kurtosis Kurtosis kurtosis-0.331
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7303000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.797; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.912; Smooth: 0.919

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6a93A01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562
Domain ID domain_id6a93B01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily10 — Cytochrome c/b562

8. Citations (1)

9. Files and Curves (10)