SAXSdb — 5np5

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

Abelson tyrosine-protein kinase 2

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 110–166	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 110–166	Fragment：SH3 domain, UNP Residues 110-166 Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	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

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 5NP5	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 mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	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
2KK1 Solution structure of C-terminal Domain of Tyrosine-protein kinase ABL2 from Homo sapiens, Northeast Structural Genomics Consortium (NESG) target HR5537A Deposited 2009-06-14	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1058–1182（125 aa） Fragment：sequence database residues 1058-1182	Not recorded	No recorded non-water small molecule	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
2XYN HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680 Deposited 2010-11-18	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 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different oligomeric state 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 mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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

8 other PDB entries and 14 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 5–61； UniProt 110–166 Author chain B； PDBConstruct 5–61； UniProt 110–166

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	5np5
Deposition date deposition_date	2017-04-13
Structure title title	Abl2 SH3 pTyr116/161
Keywords keywords	signaling, tyrosine phosphorylation, SH3 domain, kinase, 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	16.97 Å
Radius of gyration Rg (electron density) rg_electron	15.64 Å
Forward intensity I(0) i0	3970960.00
Molecular weight molecular_weight	13397.0 kDa
Excluded volume excluded_volume	16413 Å³
Envelope volume envelope_volume	19467 Å³
Hydration-shell volume shell_volume	11263 Å³
Envelope diameter envelope_diameter	58.5 Å
Shell Rg shell_rg	20.44 Å
Envelope Rg envelope_rg	15.99 Å
Shape Rg shape_rg	15.66 Å
Total Rg total_rg	16.52 Å
Total atoms total_atoms	1803
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	57.1 Å
Rg (real space) rg_real	17.02 Å
Rg uncertainty (real space) rg_real_error	0.40 Å
I(0) (real space) i0_real	3.9710e+06
I(0) uncertainty (real space) i0_real_error	5.0400e+04
Rg (reciprocal space) rg_reciprocal	17.02 Å
I(0) (reciprocal space) i0_reciprocal	3971000.0000
Solution quality estimate total_estimate	0.7855
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.0 Å
Skewness Skewness skewness	0.417
Kurtosis Kurtosis kurtosis	-0.359
Angular range angular_range	— – 0.4700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1093000.0000
Real-space data points n_real_points	77
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.761; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.925; 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	Abelson tyrosine-protein kinase 2
Molecular weight formula_weight	6926.4 kDa
EC 编号 ec_number	2.7.10.2
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2000

GSHMNLFVALYDFVASGDNTLSITKGEKLRVLGYNQNGEWSEVRSKNGQGWVPSNYITPVN

来源 Source

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

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	94

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d5np5a1
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.34.2.0 — automated matches

Domain ID domain_id	d5np5a2
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	d5np5b_
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.34.2.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5np5A00
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	5np5B00
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	30 — SH3 type barrels.
Homologous superfamily homologous superfamily	40 — SH3 Domains

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8. Citations (1)

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Unit-cell length a length_a	22.510 Å
Unit-cell length b length_b	45.910 Å
Unit-cell length c length_c	45.770 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	89.74 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	32.413 Å
R factor r_factor	0.1733
R_work r_work	0.1719
R_free r_free	0.1985

fit	/app/data/saxs_computation/np/5np5/5np5.fit
pddf	/app/data/pr_computation/np/5np5/5np5.pr.out
profile	/app/data/saxs_computation/np/5np5/5np5.dat

Abl2 SH3 pTyr116/161

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

Abelson tyrosine-protein kinase 2

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