SAXSdb — 2dco

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

S1P4 First Extracellular Loop Peptidomimetic

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 105–118 Chain A； UniProt 121–122	Fragment：Extracellular Loop 1 Mutation：L10C/A28C	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) 0.06 mol/kg；Pressure 1 NMR sample composition：1mM CCE1a U-15N; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3 NMR sample composition：3mM CCE1a U-15N,13C; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	EDG6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–26； UniProt 105–118 Author chain A； PDBConstruct 29–30； UniProt 121–122

S1P4 First Extracellular Loop Peptidomimetic

Homo sapiens

UniProt P53365

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 235–244 Chain A； UniProt 260–261 Chain A； UniProt 264–267	Fragment：Extracellular Loop 1 Mutation：L10C/A28C	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6；303 K；Ionic strength (raw mmCIF value) 0.06 mol/kg；Pressure 1 NMR sample composition：1mM CCE1a U-15N; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3 NMR sample composition：3mM CCE1a U-15N,13C; 10mM phosphate buffer pH 6; 20% TFE-d3, 0.025% NaN3 \| 20% TFE-d3	Resolution not provided

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 2DCO	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I49 CRYSTAL STRUCTURE ANALYSIS OF ARFAPTIN Deposited 2001-02-20	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；TRI-SODIUM CITRATE DIHYDRATE, ISOPROPANOL, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.275
1I4D CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP COMPLEXED WITH ARFAPTIN (P21) Deposited 2001-02-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, Peg20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.50 Å R-free 0.298
1I4L CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41) Deposited 2001-02-22	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 × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.301
1I4L CRYSTAL STRUCTURE ANALYSIS OF RAC1-GDP IN COMPLEX WITH ARFAPTIN (P41) Deposited 2001-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.70 Å R-free 0.301
1I4T CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN Deposited 2001-02-23	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 × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.304
1I4T CRYSTAL STRUCTURE ANALYSIS OF RAC1-GMPPNP IN COMPLEX WITH ARFAPTIN Deposited 2001-02-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 118–341（224 aa） Fragment：RESIDUES 118-341 Chain B 118–341（224 aa） Fragment：RESIDUES 118-341	Not recorded	MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；Tris, PEG20K, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.60 Å R-free 0.304
4DCN Crystal Structure Analysis of the Arfaptin2 BAR domain in Complex with ARL1 Deposited 2012-01-18	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 × 4 PDB declaration: tetrameric	Chain C 118–315（198 aa） Fragment：C-terminal BAR domain, residues 118-315 Chain D 118–315（198 aa） Fragment：C-terminal BAR domain, residues 118-315	Not recorded	MG MAGNESIUM ION × 2 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；298 K；100mM HEPES, 200mM Ammonium Sulfate, 25%(w/v) PEG3350, pH 7.5, vapor diffusion, temperature 298K	Resolution 3.01 Å R-free 0.333

5 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ARFP2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–12； UniProt 235–244 Author chain A； PDBConstruct 27–28； UniProt 260–261 Author chain A； PDBConstruct 31–34； UniProt 264–267

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	2dco
Deposition date deposition_date	2006-01-11
Structure title title	S1P4 First Extracellular Loop Peptidomimetic
Keywords keywords	coiled coil, disulfide, helix-turn-helix, 3-10 helix, MEMBRANE PROTEIN; MEMBRANE PROTEIN
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	9.12 Å
Radius of gyration Rg (electron density) rg_electron	9.53 Å
Forward intensity I(0) i0	26944700.00
Molecular weight molecular_weight	38862.0 kDa
Excluded volume excluded_volume	46898 Å³
Envelope volume envelope_volume	6804 Å³
Hydration-shell volume shell_volume	6208 Å³
Envelope diameter envelope_diameter	35.0 Å
Shell Rg shell_rg	14.75 Å
Envelope Rg envelope_rg	10.46 Å
Shape Rg shape_rg	9.56 Å
Total Rg total_rg	9.68 Å
Total atoms total_atoms	5190
Residues n_residues	340
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	28.4 Å
Rg (real space) rg_real	9.09 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	2.6940e+07
I(0) uncertainty (real space) i0_real_error	3.0030e+05
Rg (reciprocal space) rg_reciprocal	9.09 Å
I(0) (reciprocal space) i0_reciprocal	26940000.0000
Solution quality estimate total_estimate	0.8351
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.5 Å
Skewness Skewness skewness	0.120
Kurtosis Kurtosis kurtosis	-0.497
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11920.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.954; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	S1P4 First Extracellular Loop Peptidomimetic
Molecular weight formula_weight	3891.2 kDa
Mutation mutation	L10C/A28C
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	5190

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 BL21(DE3)

fit	/app/data/saxs_computation/dc/2dco/2dco.fit
pddf	/app/data/pr_computation/dc/2dco/2dco.pr.out
profile	/app/data/saxs_computation/dc/2dco/2dco.dat

S1P4 First Extracellular Loop Peptidomimetic

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

S1P4 First Extracellular Loop Peptidomimetic

State in the Current Structure

Other States of the Same Protein in the Database

S1P4 First Extracellular Loop Peptidomimetic

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)