3e88

Crystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors

Method: X-RAY DIFFRACTION Dmax: 100.6 Å Quality: GOOD

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

RAC-beta serine/threonine-protein kinase

Homo sapiens

UniProt P31751

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 146–480 Fragment:Akt2 kinase domain (146-480) Mutation:S474D Non-standard monomer:Yes (specific site not provided by mmCIF) Glycogen synthase kinase-3 beta peptide × 1 (P49841) G96 4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;298 K;14% PEG 2KMME, 100 mM Tris pH 8.0 and 10% ethanol diffused in. Seeded., vapor diffusion, temperature 298K Resolution 2.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 146–480 Fragment:Akt2 kinase domain (146-480) Mutation:S474D Non-standard monomer:Yes (specific site not provided by mmCIF) Glycogen synthase kinase-3 beta peptide × 1 (P49841) G96 4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;298 K;14% PEG 2KMME, 100 mM Tris pH 8.0 and 10% ethanol diffused in. Seeded., vapor diffusion, temperature 298K Resolution 2.50 Å R-free 0.273

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.

18 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name AKT2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–335; UniProt 146–480 Author chain B; PDBConstruct 1–335; UniProt 146–480

Glycogen synthase kinase-3 beta peptide

OrganismNot specified

UniProt P49841

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 3–12 Not recorded RAC-beta serine/threonine-protein kinase × 1 (P31751) G96 4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;298 K;14% PEG 2KMME, 100 mM Tris pH 8.0 and 10% ethanol diffused in. Seeded., vapor diffusion, temperature 298K Resolution 2.50 Å R-free 0.273
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 3–12 Not recorded RAC-beta serine/threonine-protein kinase × 1 (P31751) G96 4-[2-(4-amino-1,2,5-oxadiazol-3-yl)-6-{[(2R)-2-amino-3-phenylpropyl]oxy}-1-ethyl-1H-imidazo[4,5-c]pyridin-4-yl]-2-methylbut-3-yn-2-ol × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 8;298 K;14% PEG 2KMME, 100 mM Tris pH 8.0 and 10% ethanol diffused in. Seeded., vapor diffusion, temperature 298K Resolution 2.50 Å R-free 0.273

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.

114 other PDB entries and 176 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name GSK3B_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–10; UniProt 3–12 Author chain D; PDBConstruct 1–10; UniProt 3–12

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 3e88

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3e88
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3e88
Deposition date deposition_date2008-08-19
Structure title titleCrystal structures of the kinase domain of AKT2 in complex with ATP-competitive inhibitors
Keywords keywords;AKT2, kinase, GSK3 beta, ATP-binding, Nucleotide-binding, Phosphoprotein, Serine/threonine-protein kinase, Transferase, Wnt signaling pathway ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.74
Radius of gyration Rg (electron density) rg_electron30.19
Forward intensity I(0) i095264100.00
Molecular weight molecular_weight77999.0 kDa
Excluded volume excluded_volume97947 ų
Envelope volume envelope_volume122000 ų
Hydration-shell volume shell_volume34499 ų
Envelope diameter envelope_diameter106.2
Shell Rg shell_rg36.48
Envelope Rg envelope_rg30.11
Shape Rg shape_rg30.18
Total Rg total_rg30.79
Total atoms total_atoms5494
Residues n_residues658
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 dmax100.6
Rg (real space) rg_real30.85
Rg uncertainty (real space) rg_real_error0.81
I(0) (real space) i0_real9.5260e+07
I(0) uncertainty (real space) i0_real_error1.4900e+06
Rg (reciprocal space) rg_reciprocal30.81
I(0) (reciprocal space) i0_reciprocal95260000.0000
Solution quality estimate total_estimate0.8709
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.0
Skewness Skewness skewness0.414
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38700000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.922; Smooth: 0.869

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_idd3e88a_
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_idd3e88b_
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_id3e88A01
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_id3e88A02
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_id3e88B01
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_id3e88B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (2)

9. Files and Curves (10)