SAXSdb — 9uvz

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

Lysophosphatidic acid receptor 2,ARK1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–219 Chain A； UniProt 233–348	Not recorded	A1L9P 3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid × 1 NA SODIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5	Resolution 2.99 Å

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 9UVZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4P0C Crystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2 Deposited 2014-02-20	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 Monomer；Protein × 1 PDB declaration: monomeric	Chain A 347–351（5 aa） Fragment：UNP Q15599 residues 9-90; UNP Q9HBW0 residues 347-351	Not recorded	SCN THIOCYANATE ION × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；100 mM sodium acetate, 0.2 M ammonium acetate	Resolution 1.34 Å R-free 0.177

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LPAR2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 32–250； UniProt 1–219 Author chain A； PDBConstruct 638–753； UniProt 233–348

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	9uvz
Deposition date deposition_date	2025-05-11
Structure title title	Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425
Keywords keywords	GPCR, LPA2, Lysophosphatidic acid receptor 2, Ki16425, ARK1, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	34.81 Å
Radius of gyration Rg (electron density) rg_electron	35.07 Å
Forward intensity I(0) i0	179163000.00
Molecular weight molecular_weight	72084.0 kDa
Excluded volume excluded_volume	69820 Å³
Envelope volume envelope_volume	124080 Å³
Hydration-shell volume shell_volume	32240 Å³
Envelope diameter envelope_diameter	122.2 Å
Shell Rg shell_rg	37.67 Å
Envelope Rg envelope_rg	35.22 Å
Shape Rg shape_rg	35.02 Å
Total Rg total_rg	35.31 Å
Total atoms total_atoms	5474
Residues n_residues	682
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	122.3 Å
Rg (real space) rg_real	35.17 Å
Rg uncertainty (real space) rg_real_error	1.22 Å
I(0) (real space) i0_real	1.7920e+08
I(0) uncertainty (real space) i0_real_error	2.8410e+06
Rg (reciprocal space) rg_reciprocal	34.94 Å
I(0) (reciprocal space) i0_reciprocal	179100000.0000
Solution quality estimate total_estimate	0.6194
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.547
Kurtosis Kurtosis kurtosis	-0.395
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	19870000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.601; Smooth: 0.860

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Lysophosphatidic acid receptor 2,ARK1
Molecular weight formula_weight	86158.4 kDa
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	5487

MKTIIALSYIFCLVFADYKDDDDAENLYFQGMGQCYYNETIGFFYNNSGKELSSHWRPKDVVVVALGLTVSVLVLLTNLLVIAAIASNRRFHQPIYYLLGNLAAADLFAGVAYLFLMFHTGPRTARLSLEGWFLRQGLLDTSLTASVATLLAIAVERHRSVMAVQLHSRLPRGRVVMLIVGVWVAALGLGLLPAHSWHCLCALDRCSRMAPLLSRSYLAVWALSSLLVFLLMVAVYTRIFFYVRRRVQRMLELRRLLREQGEKLLKLAEESEKKIKEAIEKGEDVVKVATEETHKLIKAIWESSFEVARLLGVPEEVLEKFRKELEKLLEESKKRIEEAIKKGEDVLKVVEEEAKKLREHSEKFLETARSLGVDPRPLERLARIVRVVEESLVRIVKAIKEGEDVEKVLLSESTLIKSSIILSSGLDPREAYEELLATYEETRDSELVKEFVELVRELLRLRGEPEELVRQLDKLIEAIDRMEKAVAEGEDTLPLFLELAREILKALSDVARILAEREGLDVELIDEIVDTASRLLEEVIKKAKEGEDLDEEEEKVKKELEELKKRTEERARALGQDVELVRTIVDSLSTLLSEIVEGIKRVKEGEDPLEVLARVVLTATLQILELVRTAERRRRERTLSLVKTVVIILGAFVVCWTPGQVVLLLDGLGCESCNVLAVEKYFLLLAEANSLVNAAVYSCRDAEMRRTFRRLLCCACLRQSTRESVHYTSSAQGGASTRIMLPENGHPLMDSTLLEVLFQ

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	Homo sapiens

Entity 2 Entity 2 non-polymer

Description description	3-[[4-[4-[[(1~{R})-1-(2-chlorophenyl)ethoxy]carbonylamino]-3-methyl-1,2-oxazol-5-yl]phenyl]methylsulfanyl]propanoic acid
Molecular weight formula_weight	475.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.990 Å
Low-resolution limit resolution_low	2.990 Å
R factor r_factor	—
R_work r_work	0.3988
R_free r_free	—

Resolution resolution	2.99 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	151855

fit	/app/data/saxs_computation/uv/9uvz/9uvz.fit
pddf	/app/data/pr_computation/uv/9uvz/9uvz.pr.out
profile	/app/data/saxs_computation/uv/9uvz/9uvz.dat

Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425

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

Lysophosphatidic acid receptor 2,ARK1

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

冷冻电镜 EM 3D