SAXSdb — 7um4

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

5-hydroxytryptamine receptor 5A

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 22–357	Mutation：D65N, I278A	PGS × 1 PGE TRIETHYLENE GLYCOL × 1 PEG DI(HYDROXYETHYL)ETHER × 3 PG4 TETRAETHYLENE GLYCOL × 1 1PE PENTAETHYLENE GLYCOL × 1 NN6 ~{N}-[azanyl(azanylidene)methylidene]-5-fluoranyl-8-[2,4,6-tris(fluoranyl)phenyl]-3,4-dihydro-1~{H}-isoquinoline-2-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；0.1 M Sodium chloride, 0.1 M Lithium sulfate, 0.1 M DL-Malic acid pH 5.9, 30 % v/v PEG 400	Resolution 2.80 Å R-free 0.271

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.

Other PDB	Difference from Current Entry 7UM4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7UM5 CryoEM structure of Go-coupled 5-HT5AR in complex with 5-CT Deposited 2022-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 32–357（326 aa）	Mutation：H146P	8K3 3-(2-azanylethyl)-1H-indole-5-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.73 Å
7UM6 CryoEM structure of Go-coupled 5-HT5AR in complex with Lisuride Deposited 2022-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 32–357（326 aa）	Mutation：H146P	H8G N,N-diethyl-N'-[(8alpha)-6-methyl-9,10-didehydroergolin-8-yl]urea × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.79 Å
7UM7 CryoEM structure of Go-coupled 5-HT5AR in complex with Methylergometrine Deposited 2022-04-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 32–357（326 aa）	Mutation：H146P	H8D (8beta)-N-[(2S)-1-hydroxybutan-2-yl]-6-methyl-9,10-didehydroergoline-8-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 2.75 Å
7X5H Serotonin 5A (5-HT5A) receptor-Gi protein complex Deposited 2022-03-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 2–357（356 aa）	Not recorded	8K3 3-(2-azanylethyl)-1H-indole-5-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 3.10 Å
9W6W 5-CT-bound serotonin 5A (5-HT5A) receptor-Gi protein complex Deposited 2025-08-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain R 9–357（349 aa）	Not recorded	8K3 3-(2-azanylethyl)-1H-indole-5-carboxamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	5HT5A_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–336； UniProt 22–357

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7um4
Deposition date deposition_date	2022-04-06
Structure title title	Crystal structure of inactive 5-HT5AR in complex with AS2674723
Keywords keywords	GPCR, inactive state, MEMBRANE PROTEIN, 5-HT5AR, HTR5A; MEMBRANE PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	30.71 Å
Radius of gyration Rg (electron density) rg_electron	30.66 Å
Forward intensity I(0) i0	37465500.00
Molecular weight molecular_weight	51482.0 kDa
Excluded volume excluded_volume	65946 Å³
Envelope volume envelope_volume	82584 Å³
Hydration-shell volume shell_volume	24498 Å³
Envelope diameter envelope_diameter	105.2 Å
Shell Rg shell_rg	34.80 Å
Envelope Rg envelope_rg	30.66 Å
Shape Rg shape_rg	30.67 Å
Total Rg total_rg	31.03 Å
Total atoms total_atoms	3622
Residues n_residues	453
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	104.5 Å
Rg (real space) rg_real	31.15 Å
Rg uncertainty (real space) rg_real_error	0.95 Å
I(0) (real space) i0_real	3.7470e+07
I(0) uncertainty (real space) i0_real_error	6.1140e+05
Rg (reciprocal space) rg_reciprocal	30.97 Å
I(0) (reciprocal space) i0_reciprocal	37460000.0000
Solution quality estimate total_estimate	0.7553
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.1 Å
Skewness Skewness skewness	0.548
Kurtosis Kurtosis kurtosis	-0.569
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	9215000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.526; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.385; Smooth: 0.850

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	5-hydroxytryptamine receptor 5A
Molecular weight formula_weight	38004.4 kDa
Mutation mutation	D65N, I278A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3630

HSLGKDDLRPSSPLLSVFGVLILTLLGFLVAATFAWNLLVLATILRVRTFHRVPHNLVASMAVSNVLVAALVMPLSLVHELSGRRWQLGRRLCQLWIACDVLCCTASIWNVTAIALDRYWSITRHMEYTLRTRKCVSNVMIALTWALSAVISLAPLLFGWGETYSEGSEECQVSREPSYAVFSTVGAFYLPLCVVLFVYWKIYKAAKFRVGSRKTNSVSPISEAVEVKDSAKQPQMVFTVRHATVTFQPEGDTWREQKEQRAALMVGILIGVFVLCWAPFFLTELISPLCSCDIPAIWKSIFLWLGYSNSFFNPLIYTAFNKNYNSAFKNFFSRQH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	PGS
Molecular weight formula_weight	22251.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSHNGIDCSFWNESYLTGSRDERKKSLLSKFGMDEGVTFMFIGRFDRGQKGVDVLLKAIEILSSKKEFQEMRFIIIGKGDPELEGWARSLEEKHGNVKVITEMLSREFVRELYGSVDFVIIPSYFEPFGLVALEAMCLGAIPIASAVGGLRDIITNETGILVKAGDPGELANAILKALELSRSDLSKFRENCKKRAMSFS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	~{N}-[azanyl(azanylidene)methylidene]-5-fluoranyl-8-[2,4,6-tris(fluoranyl)phenyl]-3,4-dihydro-1~{H}-isoquinoline-2-carboxamide
Molecular weight formula_weight	366.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7um4A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1070 — Rhopdopsin 7-helix transmembrane proteins
Homologous superfamily homologous superfamily	10 — Rhodopsin 7-helix transmembrane proteins

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8. Citations (1)

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Unit-cell length a length_a	135.289 Å
Unit-cell length b length_b	42.460 Å
Unit-cell length c length_c	94.787 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	44.730 Å
R factor r_factor	0.2311
R_work r_work	0.2289
R_free r_free	0.2712

fit	/app/data/saxs_computation/um/7um4/7um4.fit
pddf	/app/data/pr_computation/um/7um4/7um4.pr.out
profile	/app/data/saxs_computation/um/7um4/7um4.dat

Crystal structure of inactive 5-HT5AR in complex with AS2674723

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

5-hydroxytryptamine receptor 5A

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)