SAXSdb — 2kk1

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

Tyrosine-protein kinase ABL2

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 1058–1182	Fragment：sequence database residues 1058-1182	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 4.5；298 K；Ionic strength (raw mmCIF value) 0.2；Pressure ambient NMR sample composition：1.2 mM [U-100% 15N] protein, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：1.2 mM [U-100% 13C; U-100% 15N] protein, 100% D2O \| 100% D2O NMR sample composition：1.2 mM [U-10% 13C; U-100% 15N] protein, 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 2KK1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ECD Solution structure of the human ABL2 SH2 domain Deposited 2007-02-13	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 163–268（106 aa） Fragment：SH2 domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 0.33mM SH2 domain U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2XYN HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 Deposited 2010-11-18	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 243–510（268 aa） Fragment：RESIDUES 243-510	Not recorded	NA SODIUM ION × 2 VX6 CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.8M SODIUM SUCCINATE, PH 7, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.81 Å R-free 0.284
2XYN HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 Deposited 2010-11-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 243–510（268 aa） Fragment：RESIDUES 243-510	Not recorded	VX6 CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.8M SODIUM SUCCINATE, PH 7, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.81 Å R-free 0.284
2XYN HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 Deposited 2010-11-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 243–510（268 aa） Fragment：RESIDUES 243-510	Not recorded	VX6 CYCLOPROPANECARBOXYLIC ACID {4-[4-(4-METHYL-PIPERAZIN-1-YL)-6-(5-METHYL-2H-PYRAZOL-3-YLAMINO)-PYRIMIDIN-2-YLSULFANYL]-PHENYL}-AMIDE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.8M SODIUM SUCCINATE, PH 7, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K	Resolution 2.81 Å R-free 0.284
3GVU The crystal structure of human ABL2 in complex with GLEEVEC Deposited 2009-03-31	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 279–546（268 aa） Fragment：Protein kinase	Not recorded	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG3350, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.05 Å R-free 0.226
3GVU The crystal structure of human ABL2 in complex with GLEEVEC Deposited 2009-03-31	Different construct Different oligomeric state 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 279–546（268 aa） Fragment：Protein kinase	Not recorded	STI 4-(4-METHYL-PIPERAZIN-1-YLMETHYL)-N-[4-METHYL-3-(4-PYRIDIN-3-YL-PYRIMIDIN-2-YLAMINO)-PHENYL]-BENZAMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG3350, 0.1M citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.05 Å R-free 0.226
3HMI The crystal structure of human ABL2 in complex with 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE Deposited 2009-05-29	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 279–546（268 aa） Fragment：Protein kinase	Not recorded	DKI 5-AMINO-3-{[4-(AMINOSULFONYL)PHENYL]AMINO}-N-(2,6-DIFLUOROPHENYL)-1H-1,2,4-TRIAZOLE-1-CARBOTHIOAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1M lithium sulfate, 0.05M di-sodium hydrogen phosphate, 0.05M citric acid, 19%(w/v) PEG 1000, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 1.65 Å R-free 0.234
3ULR Lysozyme contamination facilitates crystallization of a hetero-trimericCortactin:Arg:Lysozyme complex Deposited 2011-11-11	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 563–579（17 aa） Fragment：PXXP1 (UNP residues 563-579)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；297 K；1.0M Na Citrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.65 Å R-free 0.225
4EIH Crystal structure of Arg SH2 domain Deposited 2012-04-05	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 165–273（109 aa） Fragment：SH2 domain, UNP residues 165-273	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH8.5 100mM Tris, 15-17% PEG4000 0.2M Na Acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.20 Å R-free 0.181
5NP3 Abl2 SH3 Deposited 2017-04-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.8 M di-sodium-DL-malate	Resolution 2.00 Å R-free 0.234
5NP3 Abl2 SH3 Deposited 2017-04-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.8 M di-sodium-DL-malate	Resolution 2.00 Å R-free 0.234
5NP3 Abl2 SH3 Deposited 2017-04-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.8 M di-sodium-DL-malate	Resolution 2.00 Å R-free 0.234
5NP3 Abl2 SH3 Deposited 2017-04-13	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1.8 M di-sodium-DL-malate	Resolution 2.00 Å R-free 0.234
5NP5 Abl2 SH3 pTyr116/161 Deposited 2017-04-13	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 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；1.8 M (NH4)2SO4, 0.1 M sodium acetate	Resolution 1.40 Å R-free 0.199
5NP5 Abl2 SH3 pTyr116/161 Deposited 2017-04-13	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 110–166（57 aa） Fragment：SH3 domain, UNP Residues 110-166	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, HANGING DROP；pH 4.6；293 K；1.8 M (NH4)2SO4, 0.1 M sodium acetate	Resolution 1.40 Å R-free 0.199

8 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ABL2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 11–135； UniProt 1058–1182

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	2kk1
Deposition date deposition_date	2009-06-14
Structure title title	Solution structure of C-terminal Domain of Tyrosine-protein kinase ABL2 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) target HR5537A
Keywords keywords	;Methods development, Tyrosin protein kinase abl2, F-actin binding domain, NESG, Alternative splicing, ATP-binding, Cell adhesion, Cytoplasm, Cytoskeleton, Kinase, Lipoprotein, Magnesium, Manganese, Metal-binding, Myristate, Nucleotide-binding, Phosphoprotein, Polymorphism, SH2 domain, SH3 domain, Transferase, Tyrosine-protein kinase, Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium ;; 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	20.48 Å
Radius of gyration Rg (electron density) rg_electron	19.82 Å
Forward intensity I(0) i0	1292910000.00
Molecular weight molecular_weight	290710.0 kDa
Excluded volume excluded_volume	359430 Å³
Envelope volume envelope_volume	109030 Å³
Hydration-shell volume shell_volume	30799 Å³
Envelope diameter envelope_diameter	108.9 Å
Shell Rg shell_rg	35.83 Å
Envelope Rg envelope_rg	33.18 Å
Shape Rg shape_rg	19.86 Å
Total Rg total_rg	20.13 Å
Total atoms total_atoms	40860
Residues n_residues	2700
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	56.3 Å
Rg (real space) rg_real	18.72 Å
Rg uncertainty (real space) rg_real_error	0.16 Å
I(0) (real space) i0_real	1.2310e+09
I(0) uncertainty (real space) i0_real_error	1.5060e+07
Rg (reciprocal space) rg_reciprocal	20.89 Å
I(0) (reciprocal space) i0_reciprocal	1293000000.0000
Solution quality estimate total_estimate	0.6619
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	17.7 Å
Skewness Skewness skewness	0.490
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	1.7000
Highest regularization parameter α highest_alpha	1188000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.003; Oscil: 0.912; Stabil: 0.993; Sysdev: 0.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2kk1A01
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	120 — Four Helix Bundle (Hemerythrin (Met), subunit A)
Homologous superfamily homologous superfamily	330 — Nucleotidyltransferases domain 2

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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	Tyrosine-protein kinase ABL2
Molecular weight formula_weight	14557.5 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	40860

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

Solution structure of C-terminal Domain of Tyrosine-protein kinase ABL2 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) target HR5537A

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

Tyrosine-protein kinase ABL2

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/kk/2kk1/2kk1.fit
pddf	/app/data/pr_computation/kk/2kk1/2kk1.pr.out
profile	/app/data/saxs_computation/kk/2kk1/2kk1.dat