1o6k

Structure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP

Method: X-RAY DIFFRACTION Dmax: 66.8 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 146–481 Fragment:KINASE DOMAIN, RESIDUES 146-481 Mutation:YES Non-standard monomer:Yes (specific site not provided by mmCIF) GLYCOGEN SYNTHASE KINASE-3 BETA × 1 (P49841) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;10 MG/ML PROTEIN 20 PEG 4K, 10% ISOPROPONAL, 5 MM DTT, pH 7.50 Resolution 1.70 Å R-free 0.234

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 1–336; UniProt 146–481

GLYCOGEN SYNTHASE KINASE-3 BETA

HOMO SAPIENS

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:PEPTIDE, RESIDUES 3-12 RAC-BETA SERINE/THREONINE PROTEIN KINASE × 1 (P31751) ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 MN MANGANESE (II) ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:pH 7.5;10 MG/ML PROTEIN 20 PEG 4K, 10% ISOPROPONAL, 5 MM DTT, pH 7.50 Resolution 1.70 Å R-free 0.234

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 KG3B_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 1o6k

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1o6k
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1o6k
Deposition date deposition_date2002-10-08
Structure title titleStructure of activated form of PKB kinase domain S474D with GSK3 peptide and AMP-PNP
Keywords keywordsPROTEIN KINASE, TRANSFERASE, SERINE/THREONINE-PROTEIN KINASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.57
Radius of gyration Rg (electron density) rg_electron19.44
Forward intensity I(0) i025584300.00
Molecular weight molecular_weight38480.0 kDa
Excluded volume excluded_volume48037 ų
Envelope volume envelope_volume56051 ų
Hydration-shell volume shell_volume23247 ų
Envelope diameter envelope_diameter69.8
Shell Rg shell_rg26.70
Envelope Rg envelope_rg19.85
Shape Rg shape_rg19.45
Total Rg total_rg20.37
Total atoms total_atoms2701
Residues n_residues327
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 dmax66.8
Rg (real space) rg_real20.45
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real2.5580e+07
I(0) uncertainty (real space) i0_real_error2.9410e+05
Rg (reciprocal space) rg_reciprocal20.47
I(0) (reciprocal space) i0_reciprocal25580000.0000
Solution quality estimate total_estimate0.8035
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary26.2
Skewness Skewness skewness0.202
Kurtosis Kurtosis kurtosis-0.348
Angular range angular_range— – 0.3850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8588000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.816; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1o6ka_
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_id1o6kA01
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_id1o6kA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1

8. Citations (1)

9. Files and Curves (10)