SAXSdb — 2k79

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

SH3 domain of 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 177–237 Chain B； UniProt 238–344	Not recorded	No other associated polymer	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

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 2K79	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 mutation/modification Different oligomeric state Different experimental conditions	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 oligomeric state Different experimental conditions	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 oligomeric state Different experimental conditions	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 oligomeric state Different experimental conditions	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 oligomeric state Different experimental conditions	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 experimental conditions	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 experimental conditions	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
2K7A Ensemble Structures of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase. Deposited 2008-08-08	Parsed fields agree	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 mutation/modification Different oligomeric state Different experimental conditions	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 mutation/modification Different oligomeric state Different experimental conditions	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
3S9K Crystal structure of the Itk SH2 domain. Deposited 2011-06-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 236–344（109 aa） Fragment：SH2 domain (UNP Residues 236-344)	Not recorded	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
3S9K Crystal structure of the Itk SH2 domain. Deposited 2011-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 236–344（109 aa） Fragment：SH2 domain (UNP Residues 236-344)	Not recorded	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

11 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ITK_MOUSE
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 3–63； UniProt 177–237 Author chain B； PDBConstruct 3–109； UniProt 238–344

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	2k79
Deposition date deposition_date	2008-08-08
Structure title title	Solution Structure of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase
Keywords keywords	;SH3, SH2, novel, cis, ATP-binding, Cell membrane, Kinase, Membrane, Metal-binding, Nucleotide-binding, Phosphoprotein, SH2 domain, SH3 domain, Transferase, Tyrosine-protein kinase, Zinc, Zinc-finger ;; TRANSFERASE
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	17.97 Å
Radius of gyration Rg (electron density) rg_electron	16.65 Å
Forward intensity I(0) i0	7469650.00
Molecular weight molecular_weight	19860.0 kDa
Excluded volume excluded_volume	24796 Å³
Envelope volume envelope_volume	29926 Å³
Hydration-shell volume shell_volume	15255 Å³
Envelope diameter envelope_diameter	56.5 Å
Shell Rg shell_rg	22.48 Å
Envelope Rg envelope_rg	17.02 Å
Shape Rg shape_rg	16.61 Å
Total Rg total_rg	17.81 Å
Total atoms total_atoms	2749
Residues n_residues	171
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	58.4 Å
Rg (real space) rg_real	17.90 Å
Rg uncertainty (real space) rg_real_error	0.33 Å
I(0) (real space) i0_real	7.4700e+06
I(0) uncertainty (real space) i0_real_error	9.3800e+04
Rg (reciprocal space) rg_reciprocal	17.91 Å
I(0) (reciprocal space) i0_reciprocal	7470000.0000
Solution quality estimate total_estimate	0.8894
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	57.6 Å
Skewness Skewness skewness	0.252
Kurtosis Kurtosis kurtosis	-0.390
Angular range angular_range	— – 0.4450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2075000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.868; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	SH3 domain of Tyrosine-protein kinase ITK/TSK
Molecular weight formula_weight	7355.9 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	2749

GSPEETLVIALYDYQTNDPQELALRCDEEYYLLDSSEIHWWRVQDKNGHEGYAPSSYLVEKSP

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 polymer

Description description	SH2 domain of Tyrosine-protein kinase ITK/TSK
Molecular weight formula_weight	12678.3 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	B

GSNNLETYEWYNKSISRDKAEKLLLDTGKEGAFMVRDSRTPGTYTVSVFTKAIISENPCIKHYHIKETNDSPKRYYVAEKYVFDSIPLLIQYHQYNGGGLVTRLRYPVCG

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

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2k79a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.2 — SH3-domain
Family Family family	b.34.2.1 — SH3-domain

Domain ID domain_id	d2k79a2
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

Domain ID domain_id	d2k79b1
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	d2k79b2
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 (2 domains)

Domain ID domain_id	2k79A00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

Domain ID domain_id	2k79B00
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	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	—

fit	/app/data/saxs_computation/k7/2k79/2k79.fit
pddf	/app/data/pr_computation/k7/2k79/2k79.pr.out
profile	/app/data/saxs_computation/k7/2k79/2k79.dat

Solution Structure of the binary complex between the SH3 and SH2 domain of interleukin-2 tyrosine kinase

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

SH3 domain of 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

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (4 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)