SAXSdb — 1c07

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

PROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)

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 217–311	Fragment：EPS15 HOMOLOGY (EH) DOMAIN 3	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions：pH 7.8；298 K；Ionic strength (raw mmCIF value) 100mM KCL, 2mM CACL2, 2mM NAN3；Pressure AMBIENT NMR sample composition：0.5-1MM EH3; 20MM D-TRIS, 100MM KCL, 2MM CACL2, 2MM NAN3, 0.1MM D-DTT; 95% H2O, 5% D2O	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 1C07	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1EH2 STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15, NMR, 20 STRUCTURES Deposited 1998-07-10	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 121–218（98 aa） Fragment：EPS15 HOMOLOGY (EH) DOMAIN 2, RESIDUES 121-218	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120 MILLIMOLAR；Pressure ATMOSPHERIC NMR sample composition H2O AND D2O	Resolution not provided
1F8H STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFR Deposited 2000-06-30	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–215（95 aa） Fragment：RESIDUES 121-218 OF HUMAN EPS15	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient NMR sample composition 1 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride \| 10%/90% D2O/H2O NMR sample composition 1 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride \| 99.999% D2O NMR sample composition 0.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride \| 10%/90% D2O/H2O NMR sample composition 0.2 mM {15N}-EH2 and 5 mM peptide, 20 mM perdeuterated Tris, 100 mM potassium chloride, 1 mM perdeuterated DTT, 1 mM sodium azide 2 mM calcium chloride \| 10%/90% D2O/H2O	Resolution not provided
1FF1 STRUCTURE OF THE SECOND EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15 IN COMPLEX WITH PTGSSSTNPFL Deposited 2000-07-24	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–215（95 aa） Fragment：SECOND EH DOMAIN	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 0.15；Pressure AMBIENT NMR sample composition 1 MM {15N}-EH2 AND 5 MM PEPTIDE, 20 MM PERDEUTERATED TRIS, 100 MM POTASSIUM CHLORIDE, 1 MM PERDEUTERATED DTT, 1 MM SODIUM AZIDE, 2 MM CALCIUM CHLORIDE \| 90% H2O/10% D2O NMR sample composition 1 MM {15N}-EH2 AND 5 MM PEPTIDE, 20 MM PERDEUTERATED TRIS, 100 MM POTASSIUM CHLORIDE, 1 MM PERDEUTERATED DTT, 1 MM SODIUM AZIDE, 2 MM CALCIUM CHLORIDE \| 100% D2O	Resolution not provided
2JXC Structure of the EPS15-EH2 Stonin2 Complex Deposited 2007-11-12	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 121–215（95 aa） Fragment：EH 2 domain	Not recorded	CA CALCIUM ION × 1	SOLUTION NMR NMR measurement conditions pH 7；295 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.5-1 mM [U-99% 13C; U-99% 15N] EH2, 0.5-1 mM Stonin peptide, 2 mM CA, 100% D2O \| 100% D2O NMR sample composition 0.5-1 mM EH2, 0.5-1 mM [U-99% 13C; U-99% 15N] Stonin peptide, 2 mM CA, 100% D2O \| 100% D2O NMR sample composition 0.6 mM EH2, 0.6 mM Stonin peptide, 2 mM CA, 100% D2O \| 100% D2O	Resolution not provided
4RH5 Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 peptide Deposited 2014-10-01	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 × 2 PDB declaration: dimeric	Chain B 846–854（9 aa） Fragment：PTYR849 peptide (UNP RESIDUES 846-854)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.203
4RH9 Crystal structure of PTPN3 (PTPH1) H812F, M883G mutant in complex with Eps15 pTyr849 peptide Deposited 2014-10-01	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 × 2 PDB declaration: dimeric	Chain B 846–854（9 aa） Fragment：pTyr849 peptide (UNP RESIDUES 846-854)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.226
4RHG Crystal structure of PTPN3 (PTPH1) D811E, C842S mutant in complex with Eps15 pTyr849 peptide Deposited 2014-10-02	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 × 2 PDB declaration: dimeric	Chain B 846–854（9 aa） Fragment：pTyr849 peptide (UNP RESIDUES 846-854)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 21% PEG 8000, 5% glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.58 Å R-free 0.209
4S0G Crystal structure of PTPN3 (PTPH1) in complex with Eps15 pTyr849 P850V peptide Deposited 2014-12-31	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 × 2 PDB declaration: dimeric	Chain B 846–854（9 aa） Fragment：Phosphotyrosine 849 peptide, UNP residues 846-854	Mutation：P850V Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M Tris-HCl, 26% PEG 8000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.72 Å R-free 0.229
5JP2 Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide Deposited 2016-05-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 615–637（23 aa） Fragment：UNP Residues 615-637	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM Bis-Tris propane pH, 6.0, 200 mM sodium citrate, 22% PEG 3350 and 10 mM DTT Crystals were cryopretetcted in 22% glycerol before flash cooling	Resolution 2.40 Å R-free 0.234
5JP2 Fcho1 Mu homology domain (Danio Rerio) with bound Eps15 peptide Deposited 2016-05-03	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 615–637（23 aa） Fragment：UNP Residues 615-637	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；289 K；100 mM Bis-Tris propane pH, 6.0, 200 mM sodium citrate, 22% PEG 3350 and 10 mM DTT Crystals were cryopretetcted in 22% glycerol before flash cooling	Resolution 2.40 Å R-free 0.234

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EP15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–95； UniProt 217–311

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	1c07
Deposition date deposition_date	1999-07-14
Structure title title	STRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15
Keywords keywords	CALCIUM BINDING, SIGNALING DOMAIN, NPF BINDING, FW BINDING, EF-HAND, EH DOMAIN, SIGNALING PROTEIN; SIGNALING 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	12.06 Å
Radius of gyration Rg (electron density) rg_electron	11.93 Å
Forward intensity I(0) i0	535451000.00
Molecular weight molecular_weight	212670.0 kDa
Excluded volume excluded_volume	272590 Å³
Envelope volume envelope_volume	18776 Å³
Hydration-shell volume shell_volume	11954 Å³
Envelope diameter envelope_diameter	41.9 Å
Shell Rg shell_rg	19.16 Å
Envelope Rg envelope_rg	13.44 Å
Shape Rg shape_rg	11.87 Å
Total Rg total_rg	12.27 Å
Total atoms total_atoms	30220
Residues n_residues	1900
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	38.9 Å
Rg (real space) rg_real	11.95 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	5.3550e+08
I(0) uncertainty (real space) i0_real_error	5.6950e+06
Rg (reciprocal space) rg_reciprocal	11.95 Å
I(0) (reciprocal space) i0_reciprocal	535500000.0000
Solution quality estimate total_estimate	0.8663
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.2 Å
Skewness Skewness skewness	-0.063
Kurtosis Kurtosis kurtosis	-0.418
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	123000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.762; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.985

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1c07a_
Class class	a — All alpha proteins
Fold Fold fold	a.39 — EF Hand-like
Superfamily Superfamily superfamily	a.39.1 — EF-hand
Family Family family	a.39.1.6 — Eps15 homology domain (EH domain)

CATH v4.4 (1 domains)

Domain ID domain_id	1c07A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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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	1

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

Description description	PROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)
Molecular weight formula_weight	10626.4 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	30220

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

STRUCTURE OF THE THIRD EPS15 HOMOLOGY DOMAIN OF HUMAN EPS15

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

PROTEIN (EPIDERMAL GROWTH FACTOR RECEPTOR PATHWAY SUBSTRATE 15)

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

fit	/app/data/saxs_computation/c0/1c07/1c07.fit
pddf	/app/data/pr_computation/c0/1c07/1c07.pr.out
profile	/app/data/saxs_computation/c0/1c07/1c07.dat