SAXSdb — 3eaz

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

Tyrosine-protein kinase CSK

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 73–178	Fragment：Csk, SH2 domain (UNP residues 73 to 178) Mutation：C122S	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.3；298 K；22% PEG 4000, 100 mM Bis-Tris, pH 7.3., VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.31 Å R-free 0.226

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 3EAZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BYG KINASE DOMAIN OF HUMAN C-TERMINAL SRC KINASE (CSK) IN COMPLEX WITH INHIBITOR STAUROSPORINE Deposited 1998-10-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 173–450（278 aa） Fragment：KINASE DOMAIN	Not recorded	STU STAUROSPORINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 9；VAPOUR DIFFUSION, PROTEIN SOLUTION (10 MG/ML) CONTAINING 1MM STAUROSPORINE WAS MIXED IN 1:1 RATIO WITH THE RESERVOIR SOLUTION. THE RESERVOIR SOLUTION CONTAINED 0.2M MGCL2, 0.1M TRISHCL PH 9.0, 24% PEG 4000.	Resolution 2.40 Å R-free 0.287
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.278
1CSK THE CRYSTAL STRUCTURE OF HUMAN CSKSH3: STRUCTURAL DIVERSITY NEAR THE RT-SRC AND N-SRC LOOP Deposited 1994-03-22	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–71（71 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å R-free 0.278
3D7T Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 188–450（263 aa） Fragment：Csk kinase domain	Mutation：K361A/K362A	STU STAUROSPORINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP	Resolution 2.90 Å R-free 0.278
3D7T Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 188–450（263 aa） Fragment：Csk kinase domain	Mutation：K361A/K362A	STU STAUROSPORINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；VAPOR DIFFUSION, SITTING DROP	Resolution 2.90 Å R-free 0.278
3D7U Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 188–450（263 aa） Fragment：Csk kinase domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.11 Å R-free 0.302
3D7U Structural basis for the recognition of c-Src by its inactivator Csk Deposited 2008-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 188–450（263 aa） Fragment：Csk kinase domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 4.11 Å R-free 0.302
3EAC Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), Oxidized form. Deposited 2008-08-25	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 73–178（106 aa） Fragment：SH2 Domain (UNP residues 73 to 178)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 7.3；298 K；22% PEG 4000, 100 mM Bis-Tris, pH 7.3., EVAPORATION, temperature 298K	Resolution 1.37 Å R-free 0.217

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

View Construct and Data Evidence

UniProt name	CSK_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–106； UniProt 73–178

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	3eaz
Deposition date deposition_date	2008-08-26
Structure title title	Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), C122S mutant.
Keywords keywords	;SH2, CSK, DISULFIDE, OXIDIZED Reduced, ATP-binding, Cell membrane, Kinase, Membrane, Nucleotide-binding, Phosphoprotein, SH2 domain, SH3 domain, Transferase, Tyrosine-protein kinase ;; 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	14.38 Å
Radius of gyration Rg (electron density) rg_electron	12.92 Å
Forward intensity I(0) i0	2834300.00
Molecular weight molecular_weight	11782.0 kDa
Excluded volume excluded_volume	14784 Å³
Envelope volume envelope_volume	16376 Å³
Hydration-shell volume shell_volume	10822 Å³
Envelope diameter envelope_diameter	43.4 Å
Shell Rg shell_rg	18.62 Å
Envelope Rg envelope_rg	13.31 Å
Shape Rg shape_rg	12.90 Å
Total Rg total_rg	14.27 Å
Total atoms total_atoms	828
Residues n_residues	102
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	45.3 Å
Rg (real space) rg_real	14.28 Å
Rg uncertainty (real space) rg_real_error	0.22 Å
I(0) (real space) i0_real	2.8340e+06
I(0) uncertainty (real space) i0_real_error	2.9300e+04
Rg (reciprocal space) rg_reciprocal	14.29 Å
I(0) (reciprocal space) i0_reciprocal	2834000.0000
Solution quality estimate total_estimate	0.8886
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.5 Å
Skewness Skewness skewness	0.077
Kurtosis Kurtosis kurtosis	-0.360
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	477300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.960

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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	d3eaza_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.93 — SH2-like
Superfamily Superfamily superfamily	d.93.1 — SH2 domain
Family Family family	d.93.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	3eazA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	505 — SHC Adaptor Protein
Homologous superfamily homologous superfamily	10 — SH2 domain

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8. Citations (1)

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Unit-cell length a length_a	37.506 Å
Unit-cell length b length_b	48.148 Å
Unit-cell length c length_c	49.928 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	1.310 Å
Low-resolution limit resolution_low	25.460 Å
R factor r_factor	0.1956
R_work r_work	0.1940
R_free r_free	0.2257

Description description	Tyrosine-protein kinase CSK
Molecular weight formula_weight	12146.8 kDa
EC 编号 ec_number	2.7.10.2
Mutation mutation	C122S
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	971

Crystal structure of SH2 domain of Human Csk (carboxyl-terminal src kinase), C122S mutant.

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

Tyrosine-protein kinase CSK

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	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
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	118

fit	/app/data/saxs_computation/ea/3eaz/3eaz.fit
pddf	/app/data/pr_computation/ea/3eaz/3eaz.pr.out
profile	/app/data/saxs_computation/ea/3eaz/3eaz.dat