2x39

Structure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin- 4-yl)piperidine-4-carboxamide bound to PKB

Method: X-RAY DIFFRACTION Dmax: 64.5 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 146–467 Fragment:KINASE CATALYTIC DOMAIN, RESIDUES 146-467 Non-standard monomer:Yes (specific site not provided by mmCIF) GLYCOGEN SYNTHASE KINASE-3 BETA × 1 (P49841) X39 4-AMINO-N-(4-CHLOROBENZYL)-1-(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDINE-4-CARBOXAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.93 Å R-free 0.226

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 23 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 6–327; UniProt 146–467

GLYCOGEN SYNTHASE KINASE-3 BETA

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 Fragment:RESIDUES 3-12 RAC-BETA SERINE/THREONINE-PROTEIN KINASE × 1 (P31751) X39 4-AMINO-N-(4-CHLOROBENZYL)-1-(7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL)PIPERIDINE-4-CARBOXAMIDE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.93 Å R-free 0.226

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 177 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

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 2x39

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2x39
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2x39
Deposition date deposition_date2010-01-22
Structure title titleStructure of 4-Amino-N-(4-chlorobenzyl)-1-(7H-pyrrolo(2,3-d)pyrimidin- 4-yl)piperidine-4-carboxamide bound to PKB
Keywords keywordsSERINE/THREONINE-PROTEIN KINASE, NUCLEOTIDE-BINDING, WNT SIGNALING PATHWAY, KINASE, TRANSFERASE, PHOSPHOPROTEIN; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.69
Radius of gyration Rg (electron density) rg_electron19.45
Forward intensity I(0) i024367300.00
Molecular weight molecular_weight38288.0 kDa
Excluded volume excluded_volume48123 ų
Envelope volume envelope_volume55337 ų
Hydration-shell volume shell_volume23034 ų
Envelope diameter envelope_diameter67.8
Shell Rg shell_rg26.60
Envelope Rg envelope_rg19.78
Shape Rg shape_rg19.43
Total Rg total_rg20.48
Total atoms total_atoms2697
Residues n_residues326
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 dmax64.5
Rg (real space) rg_real20.56
Rg uncertainty (real space) rg_real_error0.37
I(0) (real space) i0_real2.4370e+07
I(0) uncertainty (real space) i0_real_error3.0560e+05
Rg (reciprocal space) rg_reciprocal20.59
I(0) (reciprocal space) i0_reciprocal24370000.0000
Solution quality estimate total_estimate0.8161
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.2
Skewness Skewness skewness0.170
Kurtosis Kurtosis kurtosis-0.397
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8926000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.875; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2x39a_
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 (2 domains)

Domain ID domain_id2x39A01
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_id2x39A02
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)