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- PDB-3cqu: Crystal Structure of Akt-1 complexed with substrate peptide and i... -

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Basic information

Entry
Database: PDB / ID: 3cqu
TitleCrystal Structure of Akt-1 complexed with substrate peptide and inhibitor
Components
  • Glycogen synthase kinase-3 beta
  • RAC-alpha serine/threonine-protein kinase
KeywordsTRANSFERASE / Kinase / Apoptosis / ATP-binding / Carbohydrate metabolism / Cytoplasm / Glucose metabolism / Glycogen biosynthesis / Glycogen metabolism / Membrane / Nucleotide-binding / Nucleus / Phosphoprotein / Serine/threonine-protein kinase / Sugar transport / Translation regulation / Transport / Alternative splicing / Wnt signaling pathway
Function / homology
Function and homology information


positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / maintenance of protein location in mitochondrion / Inhibition of TSC complex formation by AKT (PKB) ...positive regulation of endodeoxyribonuclease activity / regulation of tRNA methylation / negative regulation of protein maturation / negative regulation of fatty acid beta-oxidation / positive regulation of protein localization to endoplasmic reticulum / regulation of glycogen biosynthetic process / negative regulation of lymphocyte migration / negative regulation of protein localization to lysosome / maintenance of protein location in mitochondrion / Inhibition of TSC complex formation by AKT (PKB) / AKT-mediated inactivation of FOXO1A / cellular response to rapamycin / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / regulation of type B pancreatic cell development / activation-induced cell death of T cells / positive regulation of anaphase-promoting complex-dependent catabolic process / potassium channel activator activity / fibroblast migration / mammary gland epithelial cell differentiation / AKT phosphorylates targets in the nucleus / negative regulation of glycogen (starch) synthase activity / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of mesenchymal stem cell differentiation / negative regulation of type B pancreatic cell development / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of cilium assembly / regulation of protein export from nucleus / superior temporal gyrus development / cellular response to interleukin-3 / positive regulation of protein localization to cilium / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / negative regulation of glycogen biosynthetic process / negative regulation of TORC2 signaling / positive regulation of TORC2 signaling / positive regulation of glucose metabolic process / negative regulation of dopaminergic neuron differentiation / positive regulation of protein localization to centrosome / RUNX2 regulates genes involved in cell migration / maintenance of cell polarity / beta-arrestin-dependent dopamine receptor signaling pathway / positive regulation of protein localization to cell surface / response to fluid shear stress / interleukin-18-mediated signaling pathway / regulation of long-term synaptic potentiation / response to growth factor / heart valve development / CRMPs in Sema3A signaling / tau-protein kinase / beta-catenin destruction complex / cell migration involved in sprouting angiogenesis / negative regulation of leukocyte cell-cell adhesion / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / RAB GEFs exchange GTP for GDP on RABs / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of cilium assembly / negative regulation of calcineurin-NFAT signaling cascade / Maturation of nucleoprotein / phosphatidylinositol-3,4-bisphosphate binding / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / negative regulation of TOR signaling / complement receptor mediated signaling pathway / sphingosine-1-phosphate receptor signaling pathway / regulation of microtubule-based process / positive regulation of cell-matrix adhesion / Wnt signalosome / glycogen metabolic process / response to growth hormone / AKT phosphorylates targets in the cytosol / MTOR signalling / anoikis / regulation of postsynapse organization / regulation of axon extension / Disassembly of the destruction complex and recruitment of AXIN to the membrane / positive regulation of protein binding / negative regulation of protein localization to nucleus / regulation of neuron projection development / KSRP (KHSRP) binds and destabilizes mRNA / response to UV-A / Regulation of TP53 Activity through Association with Co-factors / ER overload response / cellular response to stress / negative regulation of Notch signaling pathway / Maturation of nucleoprotein / negative regulation of epithelial to mesenchymal transition / Mechanical load activates signaling by PIEZO1 and integrins in osteocytes / tau-protein kinase activity / Co-inhibition by CTLA4 / regulation of axonogenesis / establishment of cell polarity / TORC2 complex binding
Similarity search - Function
Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein kinase B alpha, catalytic domain / Protein Kinase B, pleckstrin homology domain / Glycogen synthase kinase 3, catalytic domain / : / Protein kinase, C-terminal / Protein kinase C terminal domain / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CQU / RAC-alpha serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsPandit, J.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: Synthesis and structure based optimization of novel Akt inhibitors
Authors: Lippa, B. / Pan, G. / Corbett, M. / Li, C. / Kauffman, G.S. / Pandit, J. / Robinson, S. / Wei, L. / Kozina, E. / Marr, E.S. / Borzillo, G. / Knauth, E. / Barbacci-Tobin, E.G. / Vincent, P. / ...Authors: Lippa, B. / Pan, G. / Corbett, M. / Li, C. / Kauffman, G.S. / Pandit, J. / Robinson, S. / Wei, L. / Kozina, E. / Marr, E.S. / Borzillo, G. / Knauth, E. / Barbacci-Tobin, E.G. / Vincent, P. / Troutman, M. / Baker, D. / Rajamohan, F. / Kakar, S. / Clark, T. / Morris, J.
History
DepositionApr 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations / Source and taxonomy
Category: database_2 / entity_src_gen ...database_2 / entity_src_gen / pdbx_entity_src_syn / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_strain / _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_common_name / _pdbx_entity_src_syn.organism_scientific / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAC-alpha serine/threonine-protein kinase
C: Glycogen synthase kinase-3 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0233
Polymers40,7312
Non-polymers2911
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-3.5 kcal/mol
Surface area15430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.487, 55.507, 93.359
Angle α, β, γ (deg.)90.000, 105.240, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein RAC-alpha serine/threonine-protein kinase / RAC-PK-alpha / Protein kinase B / PKB / C-AKT


Mass: 39608.094 Da / Num. of mol.: 1 / Fragment: Kinase and AGC-kinase C-terminal domains / Mutation: S473D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AKT1, PKB, RAC / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P31749, non-specific serine/threonine protein kinase
#2: Protein/peptide Glycogen synthase kinase-3 beta / GSK-3 beta


Mass: 1123.220 Da / Num. of mol.: 1 / Fragment: residues 3-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P49841, tau-protein kinase
#3: Chemical ChemComp-CQU / N-[2-(5-methyl-4H-1,2,4-triazol-3-yl)phenyl]-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 291.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13N7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.83 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→45.04 Å / Num. obs: 27699 / % possible obs: 99.8 % / Redundancy: 4.08 % / Rmerge(I) obs: 0.105 / Χ2: 0.96 / Net I/σ(I): 7.8 / Scaling rejects: 855
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2.02-2.093.550.3892.8966427091.0398.6
2.09-2.183.80.38131051927571.06100
2.18-2.2840.3543.41106627391.05100
2.28-2.394.160.3473.51161127701.08100
2.39-2.544.180.3063.81160427571.05100
2.54-2.744.180.2734.21162627481.07100
2.74-3.024.190.1855.51182627980.97100
3.02-3.454.230.1088.61179327680.88100
3.45-4.354.250.05317.41199128010.76100
4.35-45.044.20.04223.11206028520.7199.9

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2.2→45.04 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.884 / SU B: 8.607 / SU ML: 0.208 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.24 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1048 4.9 %RANDOM
Rwork0.203 ---
obs0.207 21499 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.406 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å21.34 Å2
2---1.34 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2731 0 22 192 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0222819
X-RAY DIFFRACTIONr_bond_other_d0.0020.022540
X-RAY DIFFRACTIONr_angle_refined_deg2.21.9723791
X-RAY DIFFRACTIONr_angle_other_deg1.10335924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3525326
X-RAY DIFFRACTIONr_chiral_restr0.1260.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023064
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02614
X-RAY DIFFRACTIONr_nbd_refined0.2610.2900
X-RAY DIFFRACTIONr_nbd_other0.260.23171
X-RAY DIFFRACTIONr_nbtor_other0.150.22131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.2154
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.227
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2830.28
X-RAY DIFFRACTIONr_mcbond_it1.1191.51641
X-RAY DIFFRACTIONr_mcangle_it1.87222650
X-RAY DIFFRACTIONr_scbond_it2.89731178
X-RAY DIFFRACTIONr_scangle_it4.4194.51141
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.398 72
Rwork0.321 1517
all-1589

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