SAXSdb — 5v54

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

5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 37–239 Chain A； UniProt 304–390 Chain B； UniProt 37–239 Chain B； UniProt 304–390	Fragment：UNP residues 37-239,UNP residues 304-390 Mutation：L138W	89F 1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine × 2	X-RAY DIFFRACTION X-ray crystallization conditions：LIPIDIC CUBIC PHASE；293 K；100mM Bis-Tris (pH7.0), 155mM Ammonium phosphate monobasic, 26% PEG300, 0.01M GSH (L-Glutathione reduced), GSSG (L-Glutathione oxidized)	Resolution 3.90 Å R-free 0.288

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 5V54	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IAQ Crystal structure of the chimeric protein of 5-HT1B-BRIL in complex with dihydroergotamine (PSI Community Target) Deposited 2012-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 33–239（207 aa） Chain A 304–390（87 aa）	Mutation：L138W, M29W, H124I, R128L Mutation：L138W, M29W, H124I, R128L	2GM Dihydroergotamine × 2	X-RAY DIFFRACTION X-ray crystallization conditions Lipid Cubic Phase (LCP)；pH 8.7；293 K；100 mM Tris pH 8.7, 32-36% (v/v) PEG400, 90 mM sodium citrate tribasic dihydrate, 120 mM ammonium sulfate , Lipid Cubic Phase (LCP), temperature 293K	Resolution 2.80 Å R-free 0.257
4IAR Crystal structure of the chimeric protein of 5-HT1B-BRIL in complex with ergotamine (PSI Community Target) Deposited 2012-12-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 33–239（207 aa） Chain A 306–390（85 aa）	Mutation：L138W, M29W, H124I, R128L Mutation：L138W, M29W, H124I, R128L	ERM Ergotamine × 1 OLB (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 1	X-RAY DIFFRACTION X-ray crystallization conditions Lipid Cubic Phase (LCP)；pH 7.5；293 K；100 mM Tris pH 7.5, 30% (v/v) PEG400, 400 mM lithium chloride , Lipid Cubic Phase (LCP), temperature 293K	Resolution 2.70 Å R-free 0.261
6G79 Coupling specificity of heterotrimeric Go to the serotonin 5-HT1B receptor Deposited 2018-04-05	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 × 4 PDB declaration: tetrameric	Chain S 34–390（357 aa）	Not recorded	EP5 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.78 Å
7C61 Crystal structure of 5-HT1B-BRIL and SRP2070_Fab complex Deposited 2020-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 33–239（207 aa） Chain A 306–390（85 aa）	Mutation：L138W,M1007W,H1102I,R1106L Mutation：L138W,M1007W,H1102I,R1106L	ERM Ergotamine × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；293 K；30% PEG400, 0.4M SODIUM THIOCYANATE, 0.1M SODIUM ACETATE PH 5.5	Resolution 3.00 Å R-free 0.290

4 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	5HT1B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–203； UniProt 37–239 Author chain A； PDBConstruct 309–395； UniProt 304–390 Author chain B； PDBConstruct 1–203； UniProt 37–239 Author chain B； PDBConstruct 309–395； UniProt 304–390

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	5v54
Deposition date deposition_date	2017-03-13
Structure title title	Crystal structure of 5-HT1B receptor in complex with methiothepin
Keywords keywords	5-hydroxytryptamine, GPCR antagonist, OB1, ELECTRON TRANSPORT; ELECTRON TRANSPORT
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	36.19 Å
Radius of gyration Rg (electron density) rg_electron	34.98 Å
Forward intensity I(0) i0	107439000.00
Molecular weight molecular_weight	87678.0 kDa
Excluded volume excluded_volume	111940 Å³
Envelope volume envelope_volume	148130 Å³
Hydration-shell volume shell_volume	37664 Å³
Envelope diameter envelope_diameter	145.3 Å
Shell Rg shell_rg	38.32 Å
Envelope Rg envelope_rg	35.22 Å
Shape Rg shape_rg	34.95 Å
Total Rg total_rg	35.38 Å
Total atoms total_atoms	6180
Residues n_residues	765
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	137.4 Å
Rg (real space) rg_real	36.56 Å
Rg uncertainty (real space) rg_real_error	1.61 Å
I(0) (real space) i0_real	1.0740e+08
I(0) uncertainty (real space) i0_real_error	1.9430e+06
Rg (reciprocal space) rg_reciprocal	36.33 Å
I(0) (reciprocal space) i0_reciprocal	107400000.0000
Solution quality estimate total_estimate	0.7896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.7 Å
Skewness Skewness skewness	0.635
Kurtosis Kurtosis kurtosis	0.262
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13500000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.598; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.689; Smooth: 0.778

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B
Molecular weight formula_weight	44965.2 kDa
Mutation mutation	L138W
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	6180

DYIYQDSISLPWKVLLVMLLALITLATTLSNAFVIATVYRTRKLHTPANYLIASLAVTDLLVSILVMPISTMYTVTGRWTLGQVVCDFWLSSDITCCTASIWHLCVIALDRYWAITDAVEYSAKRTPKRAAVMIALVWVFSISISLPPFFWRQAKAEEEVSECVVNTDHILYTVYSTVGAFYFPTLLLIALYGRIYVEARSRIADLEDRWRTLEDNLRVIERAANAAEVREALTRMRAAAEDAQRATPPALEDRSPASPEMEDFRHGFDILVGQIDDALRLADEGRVAEAQAAAEELRTTRNAYIQKYLMAARERKATKTLGIILGAFIVCWLPFFIISLVMPICKDACWFHLAIFDFFTWLGYLNSLINPIIYTMSNEDFKQAFHKLIRFKCTS

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 non-polymer

Description description	1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine
Molecular weight formula_weight	356.5 kDa
Source method src_method	syn
Copy count entity_count	2

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8. Citations (1)

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Unit-cell length a length_a	235.200 Å
Unit-cell length b length_b	48.830 Å
Unit-cell length c length_c	139.220 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	124.07 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.900 Å
Low-resolution limit resolution_low	45.506 Å
R factor r_factor	0.2728
R_work r_work	0.2720
R_free r_free	0.2881

fit	/app/data/saxs_computation/v5/5v54/5v54.fit
pddf	/app/data/pr_computation/v5/5v54/5v54.pr.out
profile	/app/data/saxs_computation/v5/5v54/5v54.dat

Crystal structure of 5-HT1B receptor in complex with methiothepin

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

5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)