SAXSdb — 4p0c

▼

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein

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	Insufficient information Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 9–90	Fragment：UNP Q15599 residues 9-90; UNP Q9HBW0 residues 347-351	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

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 4P0C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2D11 Crystal structure of the Radixin FERM domain complexed with the NHERF-2 C-terminal tail peptide Deposited 2005-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 310–337（28 aa） Fragment：residues 310-337	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.278
2D11 Crystal structure of the Radixin FERM domain complexed with the NHERF-2 C-terminal tail peptide Deposited 2005-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 310–337（28 aa） Fragment：residues 310-337	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.278
2D11 Crystal structure of the Radixin FERM domain complexed with the NHERF-2 C-terminal tail peptide Deposited 2005-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 310–337（28 aa） Fragment：residues 310-337	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.278
2D11 Crystal structure of the Radixin FERM domain complexed with the NHERF-2 C-terminal tail peptide Deposited 2005-08-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 310–337（28 aa） Fragment：residues 310-337	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；10% PEG4000, 5% Isopropanol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.81 Å R-free 0.278
2HE4 The crystal structure of the second PDZ domain of human NHERF-2 (SLC9A3R2) interacting with a mode 1 PDZ binding motif Deposited 2006-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 147–232（86 aa） Fragment：PDZ 2 Domain (Residues 147-230)	Mutation：D229G	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.45 Å R-free 0.180
2OCS The crystal structure of the first PDZ domain of human NHERF-2 (SLC9A3R2) Deposited 2006-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 9–91（83 aa）	Not recorded	SCN THIOCYANATE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；298 K；20% PEG 3350, 0.20M KSCN, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.50 Å R-free 0.198

3 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NHRF2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–83； UniProt 9–90

Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein

Homo sapiens

UniProt Q9HBW0

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 347–351	Fragment：UNP Q15599 residues 9-90; UNP Q9HBW0 residues 347-351	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

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 4P0C	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9UVZ Cryo-EM structure of Lysophosphatidic acid receptor 2 (LPA2)-ARK1 with Ki16425 Deposited 2025-05-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–219（219 aa） Chain A 233–348（116 aa）	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

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 84–88； UniProt 347–351

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	4p0c
Deposition date deposition_date	2014-02-20
Structure title title	Crystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2
Keywords keywords	PDZ, protein-protein interaction, PROTEIN BINDING; PROTEIN BINDING
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	14.13 Å
Radius of gyration Rg (electron density) rg_electron	12.71 Å
Forward intensity I(0) i0	2378960.00
Molecular weight molecular_weight	9828.0 kDa
Excluded volume excluded_volume	12009 Å³
Envelope volume envelope_volume	14347 Å³
Hydration-shell volume shell_volume	9872 Å³
Envelope diameter envelope_diameter	50.3 Å
Shell Rg shell_rg	18.11 Å
Envelope Rg envelope_rg	13.34 Å
Shape Rg shape_rg	12.67 Å
Total Rg total_rg	14.03 Å
Total atoms total_atoms	1362
Residues n_residues	88
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

▼

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

Maximum dimension Dmax dmax	50.8 Å
Rg (real space) rg_real	14.07 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	2.3790e+06
I(0) uncertainty (real space) i0_real_error	2.3630e+04
Rg (reciprocal space) rg_reciprocal	14.07 Å
I(0) (reciprocal space) i0_reciprocal	2379000.0000
Solution quality estimate total_estimate	0.8197
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.282
Kurtosis Kurtosis kurtosis	0.075
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	402300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.568; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.962

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein
Molecular weight formula_weight	9801.2 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	1524

MPRLCRLVRGEQGYGFHLHGEKGRRGQFIRRVEPGSPAEAAALRAGDRLVEVNGVNVEGETHHQVVQRIKAVEGQTRLLVVDQMDSTL

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	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	THIOCYANATE ION
Molecular weight formula_weight	58.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	141

▼

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d4p0ca1
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.1 — PDZ domain

Domain ID domain_id	d4p0ca2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	4p0cA00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	26.360 Å
Unit-cell length b length_b	40.250 Å
Unit-cell length c length_c	37.100 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.42 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.339 Å
Low-resolution limit resolution_low	24.208 Å
R factor r_factor	0.1466
R_work r_work	0.1449
R_free r_free	0.1769

fit	/app/data/saxs_computation/p0/4p0c/4p0c.fit
pddf	/app/data/pr_computation/p0/4p0c/4p0c.pr.out
profile	/app/data/saxs_computation/p0/4p0c/4p0c.dat

Crystal Structure of NHERF2 PDZ1 Domain in Complex with LPA2

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

Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein

State in the Current Structure

Other States of the Same Protein in the Database

Na(+)/H(+) exchange regulatory cofactor NHE-RF2/Lysophosphatidic acid receptor 2 chimeric protein

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)