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2xyn

HUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680

Method: X-RAY DIFFRACTION Dmax: 97.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

TYROSINE-PROTEIN KINASE ABL2

HOMO SAPIENS

UniProt P42684

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 243–510 Fragment：RESIDUES 243-510 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 243–510 Fragment：RESIDUES 243-510 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 243–510 Fragment：RESIDUES 243-510 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

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 2XYN 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 ligand/ion 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 ligand/ion 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
3GVU The crystal structure of human ABL2 in complex with GLEEVEC Deposited 2009-03-31 Different construct 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 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 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 oligomeric state Different ligand/ion 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 ligand/ion 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 13 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 25–292； UniProt 243–510 Author chain B； PDBConstruct 25–292； UniProt 243–510 Author chain C； PDBConstruct 25–292； UniProt 243–510

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.

SAXS scattering curve SAXS Profile

SAXS profile for 2xyn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2xyn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2xyn
Deposition date deposition_date2010-11-18
Structure title titleHUMAN ABL2 IN COMPLEX WITH AURORA KINASE INHIBITOR VX-680
Keywords keywordsCELL ADHESION, STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier30.76 Å
Radius of gyration Rg (electron density) rg_electron30.07 Å
Forward intensity I(0) i0117323000.00
Molecular weight molecular_weight86018.0 kDa
Excluded volume excluded_volume107400 ų
Envelope volume envelope_volume139970 ų
Hydration-shell volume shell_volume38762 ų
Envelope diameter envelope_diameter104.1 Å
Shell Rg shell_rg37.32 Å
Envelope Rg envelope_rg29.78 Å
Shape Rg shape_rg30.08 Å
Total Rg total_rg30.72 Å
Total atoms total_atoms6072
Residues n_residues790
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax97.9 Å
Rg (real space) rg_real30.66 Å
Rg uncertainty (real space) rg_real_error0.70 Å
I(0) (real space) i0_real1.1730e+08
I(0) uncertainty (real space) i0_real_error1.8050e+06
Rg (reciprocal space) rg_reciprocal30.71 Å
I(0) (reciprocal space) i0_reciprocal117300000.0000
Solution quality estimate total_estimate0.8996
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness0.216
Kurtosis Kurtosis kurtosis-0.466
Angular range angular_range— – 0.2600 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha31460000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.931; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.898
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

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7. Fold Classification (SCOP + CATH) 9 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2xyna_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd2xynb_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd2xync_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (6 domains)

Domain ID domain_id2xynA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2xynA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2xynB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2xynB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id2xynC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id2xynC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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8. Citations (1)

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9. Files and Curves (10)