SAXSdb — 3s9k

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

Tyrosine-protein kinase ITK/TSK

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 236–344	Fragment：SH2 domain (UNP Residues 236-344)	CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；0.1 M Sodium citrate, 10 % iso-propanol, 20 % w/v PEG 4000, 2 mM DTT with 12.5 mM Glycyl-glycyl-glycine as an additive, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.283
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 236–344	Fragment：SH2 domain (UNP Residues 236-344)	CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.3；298 K；0.1 M Sodium citrate, 10 % iso-propanol, 20 % w/v PEG 4000, 2 mM DTT with 12.5 mM Glycyl-glycyl-glycine as an additive, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.35 Å R-free 0.283

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 3S9K	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AWJ INTRAMOLECULAR ITK-PROLINE COMPLEX, NMR, MINIMIZED AVERAGE STRUCTURE Deposited 1997-10-02	Different construct 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 160–236（77 aa） Fragment：SH3-PROLINE DOMAINS	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K	Resolution not provided
1LUI NMR Structures of Itk SH2 domain, Pro287cis isoform, ensemble of 20 low energy structures Deposited 2002-05-22	Different construct Different mutation/modification 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 238–344（107 aa） Fragment：src homology 2 (SH2) domain (residues 238-344)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1 mM Itk SH2 domain U-15N, U-13C, 125 mM Phosphate buffer, pH 7.4, 2 mM DTT \| 90% H20, 10% D20 NMR sample composition 1 mM Itk SH2 domain U-15N, 125 mM Phosphate buffer, pH 7.4, 2 mM DTT \| 90% H20, 10% D20 NMR sample composition 1 mM Itk SH2 domain, 125 mM Phosphate buffer, pH 7.4, 2 mM DTT \| 90% H20, 10% D20	Resolution not provided
1LUK NMR Structure of the Itk SH2 domain, Pro287cis, Energy minimized average structure Deposited 2002-05-22	Different construct Different mutation/modification 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 238–344（107 aa） Fragment：src homology 2 (SH2) domain (residues 238-344)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1 mM Itk SH2, U-15N,13C, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, U-15N, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O	Resolution not provided
1LUM NMR Structure of the Itk SH2 domain, Pro287trans, 20 low energy structures Deposited 2002-05-22	Different construct Different mutation/modification 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 238–344（107 aa） Fragment：src homology 2 (SH2) domain (residues 238-344)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1 mM Itk SH2, U-15N,13C, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, U-15N, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O	Resolution not provided
1LUN NMR Structure of the Itk SH2 domain, Pro287trans, energy minimized average structure Deposited 2002-05-22	Different construct Different mutation/modification 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 238–344（107 aa） Fragment：src homology 2 (SH2) domain (residues 238-344)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1 mM Itk SH2, U-15N,13C, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, U-15N, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 1 mM Itk SH2, 125mM phosphate buffer, pH 7.4 \| 90% H2O/10% D2O	Resolution not provided
2ETZ The NMR minimized average structure of the Itk SH2 domain bound to a phosphopeptide Deposited 2005-10-27	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 A 238–344（107 aa） Fragment：SH2 domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90% H2O/10% D2O NMR sample composition U-15N labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90% H2O/10% D2O NMR sample composition U-15N, 13-C labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90%H20, 10%D2O NMR sample composition 5mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90%H20, 10%D2O NMR sample composition 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 100% D2O	Resolution not provided
2EU0 The NMR ensemble structure of the Itk SH2 domain bound to a phosphopeptide Deposited 2005-10-27	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 A 238–344（107 aa） Fragment：SH2 domain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 125mM；Pressure ambient NMR sample composition 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90% H2O/10% D2O NMR sample composition U-15N labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90% H2O/10% D2O NMR sample composition U-15N, 13-C labeled, 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90% H2O/10% D2O NMR sample composition 5mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 90%H20, 10%D2O NMR sample composition 1mM Itk SH2 domain, 20mM phosphopeptide, 50mM KH2PO4, 75mM NaCl, 2mM DTT, 0.02% NaN3, pH 7.4 \| 100% D2O	Resolution not provided
2K79 Solution Structure of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase Deposited 2008-08-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 177–237（61 aa） Chain B 238–344（107 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 75；Pressure ambient NMR sample composition 3.4 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 1.5 mM Itk SH2 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 3.4 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 1.5 mM Itk SH3 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 3.4 mM Itk SH3 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 3.4 mM Itk SH2 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2K7A Ensemble Structures of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase. Deposited 2008-08-08	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 177–237（61 aa） Chain B 238–344（107 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 75；Pressure ambient NMR sample composition 3.4 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 1.5 mM Itk SH2 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 3.4 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 1.5 mM Itk SH3 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] Itk SH2 domain, 3.4 mM Itk SH3 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 1.5 mM [U-100% 13C; U-100% 15N] Itk SH3 domain, 3.4 mM Itk SH2 domain, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2RN8 NMR structure note: murine Itk SH3 domain Deposited 2007-12-08	Different construct 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 177–238（62 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 75 mM NaCl；Pressure ambient NMR sample composition 3.4mM [U-100% 13C; U-100% 15N] Itk Sh3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2RNA Itk SH3 average minimized Deposited 2007-12-08	Different construct 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 177–238（62 aa） Fragment：SH3 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 75mM NaCl；Pressure ambient NMR sample composition 3.4mM [U-100% 13C; U-100% 15N] Itk Sh3, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

11 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITK_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–110； UniProt 236–344

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	3s9k
Deposition date deposition_date	2011-06-01
Structure title title	Crystal structure of the Itk SH2 domain.
Keywords keywords	proline isomerization, cis proline, domain swapped dimer, SH2 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	18.61 Å
Radius of gyration Rg (electron density) rg_electron	17.73 Å
Forward intensity I(0) i0	3570690.00
Molecular weight molecular_weight	13360.0 kDa
Excluded volume excluded_volume	16730 Å³
Envelope volume envelope_volume	22049 Å³
Hydration-shell volume shell_volume	11479 Å³
Envelope diameter envelope_diameter	63.7 Å
Shell Rg shell_rg	22.18 Å
Envelope Rg envelope_rg	18.21 Å
Shape Rg shape_rg	17.71 Å
Total Rg total_rg	18.67 Å
Total atoms total_atoms	943
Residues n_residues	114
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	63.2 Å
Rg (real space) rg_real	18.73 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	3.5710e+06
I(0) uncertainty (real space) i0_real_error	4.3790e+04
Rg (reciprocal space) rg_reciprocal	18.71 Å
I(0) (reciprocal space) i0_reciprocal	3571000.0000
Solution quality estimate total_estimate	0.7966
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.483
Kurtosis Kurtosis kurtosis	-0.186
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	362100.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.833; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.855; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Tyrosine-protein kinase ITK/TSK
Molecular weight formula_weight	13540.3 kDa
EC 编号 ec_number	2.7.10.2
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	960

GSPNNLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCGSPGIHRD

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	CITRIC ACID
Molecular weight formula_weight	192.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	17

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3s9ka1
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.93.1.1 — SH2 domain

Domain ID domain_id	d3s9ka2
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	3s9kA01
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 (2)

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Unit-cell length a length_a	53.640 Å
Unit-cell length b length_b	57.360 Å
Unit-cell length c length_c	83.190 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	8

Space group space_group	I 2 2 2
Space-group number int_tables_number	23
Crystal system crystal_system	—

Resolution resolution	2.354 Å
Low-resolution limit resolution_low	47.223 Å
R factor r_factor	0.2375
R_work r_work	0.2326
R_free r_free	0.2827

fit	/app/data/saxs_computation/s9/3s9k/3s9k.fit
pddf	/app/data/pr_computation/s9/3s9k/3s9k.pr.out
profile	/app/data/saxs_computation/s9/3s9k/3s9k.dat

Crystal structure of the Itk SH2 domain.

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

Tyrosine-protein kinase ITK/TSK

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