2v7a

Crystal structure of the T315I Abl mutant in complex with the inhibitor PHA-739358

Method: X-RAY DIFFRACTION Dmax: 149.9 Å Quality: SUSPICIOUS

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

PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1

HOMO SAPIENS

UniProt P00519

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 229–512 Fragment:KINASE DOMAIN, RESIDUES 229-512 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) 627 N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:20% PEG 4000 ,1M HEPES PH 7.0, 0.1 M MGCL2, Resolution 2.50 Å R-free 0.246
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 229–512 Fragment:KINASE DOMAIN, RESIDUES 229-512 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) 627 N-[(3E)-5-[(2R)-2-METHOXY-2-PHENYLACETYL]PYRROLO[3,4-C]PYRAZOL-3(5H)-YLIDENE]-4-(4-METHYLPIPERAZIN-1-YL)BENZAMIDE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:20% PEG 4000 ,1M HEPES PH 7.0, 0.1 M MGCL2, Resolution 2.50 Å R-free 0.246

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.

80 other PDB entries and 155 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ABL1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–286; UniProt 229–512 Author chain B; PDBConstruct 3–286; UniProt 229–512

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 2v7a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2v7a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2v7a
Deposition date deposition_date2007-07-27
Structure title titleCrystal structure of the T315I Abl mutant in complex with the inhibitor PHA-739358
Keywords keywords;KINASE, NUCLEUS, MYRISTATE, CYTOPLASM, MANGANESE, CELL ADHESION, METAL-BINDING, PROTO-ONCOGENE, TYROSINE-PROTEIN KINASE, CHROMOSOMAL REARRANGEMENT, TRANSFERASE, LIPOPROTEIN, POLYMORPHISM, CYTOSKELETON, MAGNESIUM, SH2 DOMAIN, SH3 DOMAIN, ATP-BINDING, NUCLEOTIDE-BINDING, ALTERNATIVE SPLICING, PHOSPHORYLATION, KINASE INHIBITOR, T315I ABL MUTANT ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier46.89
Radius of gyration Rg (electron density) rg_electron47.01
Forward intensity I(0) i056416500.00
Molecular weight molecular_weight63612.0 kDa
Excluded volume excluded_volume80065 ų
Envelope volume envelope_volume125310 ų
Hydration-shell volume shell_volume21993 ų
Envelope diameter envelope_diameter139.7
Shell Rg shell_rg54.35
Envelope Rg envelope_rg43.72
Shape Rg shape_rg47.02
Total Rg total_rg47.31
Total atoms total_atoms4472
Residues n_residues539
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax149.9
Rg (real space) rg_real47.46
Rg uncertainty (real space) rg_real_error1.67
I(0) (real space) i0_real5.6420e+07
I(0) uncertainty (real space) i0_real_error1.0890e+06
Rg (reciprocal space) rg_reciprocal46.90
I(0) (reciprocal space) i0_reciprocal56380000.0000
Solution quality estimate total_estimate0.3384
Solution quality rating solution_quality SUSPICIOUS a SUSPICIOUS solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary22.0
Skewness Skewness skewness0.127
Kurtosis Kurtosis kurtosis-1.510
Angular range angular_range— – 0.1700 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2540000.0000
Real-space data points n_real_points35
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.001; Stabil: 1.000; Sysdev: 0.115; Positv: 1.000; Valcen: 0.048; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2v7aa_
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_idd2v7ab_
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 (4 domains)

Domain ID domain_id2v7aA01
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_id2v7aA02
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_id2v7aB01
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_id2v7aB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)