SAXSdb — 1b0x

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

PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)

Mus musculus

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 888–981	Fragment：SAM DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；pH 7.5	Resolution 2.00 Å R-free 0.278

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 1B0X	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2XYU Crystal structure of EphA4 kinase domain in complex with VUF 12058 Deposited 2010-11-19	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 612–896（285 aa） Fragment：KINASE DOMAIN, RESIDUES 1548-1832	Not recorded	GOL GLYCEROL × 6 Q9G 5-(5-FLUORO-2-METHYLPHENYL)-6,7,8,9-TETRAHYDRO-3H-PYRAZOLO[3,4-C]ISOQUINOLIN-1-AMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.5；AMMONIUM SULFATE, BISTRIS PH 5.5, PEG 10K	Resolution 2.12 Å R-free 0.230
2Y6M Crystal structure of EphA4 kinase domain Deposited 2011-01-25	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 606–896（291 aa） Fragment：KINASE DOMAIN, RESIDUES 606-896	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions AMMONIUM SULFATE, BIS TRIS PH5.5, PEG 10 K	Resolution 1.70 Å R-free 0.203
2Y6O Crystal structure of EphA4 kinase domain in complex with Dasatinib. Deposited 2011-01-25	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 606–896（291 aa） Fragment：KINASE DOMAIN, RESIDUES 606-896	Not recorded	1N1 N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；AMMONIUM SULFATE, BIS TRIS PH 5.5, PEG 10K	Resolution 1.54 Å R-free 0.201

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

View Construct and Data Evidence

UniProt name	EPHA4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–94； UniProt 888–981

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	1b0x
Deposition date deposition_date	1998-11-14
Structure title title	THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MECHANISM FOR MODULAR DIMERIZATION.
Keywords keywords	RECEPTOR TYROSINE KINASE, PROTEIN INTERACTION MODULE, DIMERIZATION DOMAIN, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	13.45 Å
Radius of gyration Rg (electron density) rg_electron	11.98 Å
Forward intensity I(0) i0	1537340.00
Molecular weight molecular_weight	8027.0 kDa
Excluded volume excluded_volume	9947 Å³
Envelope volume envelope_volume	11322 Å³
Hydration-shell volume shell_volume	8519 Å³
Envelope diameter envelope_diameter	43.4 Å
Shell Rg shell_rg	17.02 Å
Envelope Rg envelope_rg	12.38 Å
Shape Rg shape_rg	11.98 Å
Total Rg total_rg	13.26 Å
Total atoms total_atoms	695
Residues n_residues	72
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	45.6 Å
Rg (real space) rg_real	13.40 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	1.5370e+06
I(0) uncertainty (real space) i0_real_error	1.6330e+04
Rg (reciprocal space) rg_reciprocal	13.41 Å
I(0) (reciprocal space) i0_reciprocal	1537000.0000
Solution quality estimate total_estimate	0.8561
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.259
Kurtosis Kurtosis kurtosis	-0.137
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	236000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.714; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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	d1b0xa_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.2 — SAM (sterile alpha motif) domain

CATH v4.4 (1 domains)

Domain ID domain_id	1b0xA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

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8. Citations (1)

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Unit-cell length a length_a	77.140 Å
Unit-cell length b length_b	77.140 Å
Unit-cell length c length_c	24.370 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 64
Space-group number int_tables_number	172
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2290
R_free r_free	0.2780

Description description	PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)
Molecular weight formula_weight	10265.5 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	748

THE CRYSTAL STRUCTURE OF AN EPH RECEPTOR SAM DOMAIN REVEALS A MECHANISM FOR MODULAR DIMERIZATION.

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

PROTEIN (EPHA4 RECEPTOR TYROSINE KINASE)

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

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)

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	53

fit	/app/data/saxs_computation/b0/1b0x/1b0x.fit
pddf	/app/data/pr_computation/b0/1b0x/1b0x.pr.out
profile	/app/data/saxs_computation/b0/1b0x/1b0x.dat