SAXSdb — 4z34

▼

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

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	;{1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1 H-pyrrol-3-yl}acetic acid ; × 1 (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	C562_ECOLX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 251–292； UniProt 23–64 Author chain A； PDBConstruct 301–355； UniProt 73–127

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

Homo sapiens

UniProt Q92633

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Monomer	Protein 1	;{1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1 H-pyrrol-3-yl}acetic acid ; × 1 (2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LPAR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 20–250； UniProt 2–232 Author chain A； PDBConstruct 357–435； UniProt 248–326

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	4z34
Deposition date deposition_date	2015-03-30
Structure title title	Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307
Keywords keywords	;human lysophosphatidic acid receptor 1 (LPA1), G-protein coupled receptor (GPCR), membrane protein, antagonist, endogenous ligand, PSI-biology, structural genomics, GPCR network, lipidic cubic phase (LCP), Compound design, polypharmacology, lipid receptor, TRANSPORT PROTEIN-inhibitor complex ;; TRANSPORT PROTEIN/inhibitor
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4z34__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4z34__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4z34__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	28.98 Å
Rg (electron density)	28.22 Å
Total Rg	28.70 Å
Atom count	3047
Residues	385
Excluded volume	55325 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4z34__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Lysophosphatidic acid receptor 1, Soluble cytochrome b562
Molecular weight formula_weight	52614.2 kDa
Mutation mutation	M1007W, H1102I, R1106L
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	3047

MKTIIALSYIFCLVFAGAPAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKLVMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGPNTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVIWTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGYVADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKTTRNAYIQKYLRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLAYEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILGRPLEVLFQGPHHHHHHHHHHDYKDDDDK

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	;{1-[(2S,3S)-2-(2,3-dihydro-1H-inden-2-ylmethyl)-3-(3,5-dimethoxy-4-methylphenyl)-3-hydroxypropyl]-4-(methoxycarbonyl)-1 H-pyrrol-3-yl}acetic acid ;
Molecular weight formula_weight	521.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	(2S)-2,3-dihydroxypropyl (7Z)-tetradec-7-enoate
Molecular weight formula_weight	300.4 kDa
Source method src_method	syn
Copy count entity_count	1

▶

Unit-cell length a length_a	34.280 Å
Unit-cell length b length_b	112.150 Å
Unit-cell length c length_c	154.630 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 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.2556
R_work r_work	0.2543
R_free r_free	0.2805

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307

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

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4z34__assembly_1__model_1

4z34__assembly_1__model_1 | I(q)

4z34__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)

Crystal Structure of Human Lysophosphatidic Acid Receptor 1 in complex with ONO9780307

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

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Lysophosphatidic acid receptor 1, Soluble cytochrome b562

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4z34__assembly_1__model_1

4z34__assembly_1__model_1 | I(q)

4z34__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

7. Citations (1)