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

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Basic information

Entry
Database: PDB / ID: 3cqw
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


regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels ...regulation of tRNA methylation / negative regulation of protein maturation / response to insulin-like growth factor stimulus / regulation of glycogen biosynthetic process / negative regulation of protein localization to lysosome / positive regulation of protein localization to endoplasmic reticulum / negative regulation of lymphocyte migration / cellular response to rapamycin / maintenance of protein location in mitochondrion / cellular response to decreased oxygen levels / maternal placenta development / regulation of type B pancreatic cell development / AKT-mediated inactivation of FOXO1A / negative regulation of long-chain fatty acid import across plasma membrane / Negative regulation of the PI3K/AKT network / potassium channel activator activity / establishment of protein localization to mitochondrion / AKT phosphorylates targets in the nucleus / negative regulation of fatty acid beta-oxidation / neuron projection organization / regulation of microtubule anchoring at centrosome / negative regulation of type B pancreatic cell development / negative regulation of glycogen (starch) synthase activity / negative regulation of mesenchymal stem cell differentiation / superior temporal gyrus development / cellular response to oxidised low-density lipoprotein particle stimulus / negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway / negative regulation of cilium assembly / cellular response to peptide / positive regulation of protein localization to cilium / negative regulation of glycogen biosynthetic process / Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA / negative regulation of TORC2 signaling / negative regulation of dopaminergic neuron differentiation / maintenance of cell polarity / positive regulation of organ growth / positive regulation of TORC2 signaling / positive regulation of protein localization to centrosome / RUNX2 regulates genes involved in cell migration / interleukin-18-mediated signaling pathway / positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / response to fluid shear stress / fibroblast migration / MTOR signalling / positive regulation of cilium assembly / positive regulation of sodium ion transport / mammary gland epithelial cell differentiation / response to growth factor / beta-catenin destruction complex / positive regulation of glucose metabolic process / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / CRMPs in Sema3A signaling / heart valve development / tau-protein kinase / cellular response to granulocyte macrophage colony-stimulating factor stimulus / RAB GEFs exchange GTP for GDP on RABs / regulation of microtubule-based process / phosphatidylinositol-3,4-bisphosphate binding / regulation of protein export from nucleus / negative regulation of leukocyte cell-cell adhesion / positive regulation of protein localization to cell surface / peripheral nervous system myelin maintenance / 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 / glycogen biosynthetic process / Maturation of nucleoprotein / cellular response to interleukin-3 / sphingosine-1-phosphate receptor signaling pathway / positive regulation of endodeoxyribonuclease activity / response to growth hormone / regulation of long-term synaptic potentiation / Wnt signalosome / cell migration involved in sprouting angiogenesis / negative regulation of TOR signaling / positive regulation of fibroblast migration / anoikis / protein serine/threonine kinase inhibitor activity / mammalian oogenesis stage / negative regulation of protein localization to nucleus / regulation of postsynapse organization / labyrinthine layer blood vessel development / Disassembly of the destruction complex and recruitment of AXIN to the membrane / AKT phosphorylates targets in the cytosol / activation-induced cell death of T cells / TORC2 complex binding / negative regulation of calcineurin-NFAT signaling cascade / regulation of axon extension / Maturation of nucleoprotein / regulation of myelination / response to food / G protein-coupled dopamine receptor signaling pathway / negative regulation of epithelial to mesenchymal transition / response to UV-A / tau-protein kinase activity
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-CQW / : / RAC-alpha serine/threonine-protein kinase / Glycogen synthase kinase-3 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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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)41,0614
Polymers40,7312
Non-polymers3302
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-5.8 kcal/mol
Surface area15580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.505, 55.879, 92.864
Angle α, β, γ (deg.)90.000, 102.360, 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-CQW / 5-(5-chloro-7H-pyrrolo[2,3-d]pyrimidin-4-yl)-4,5,6,7-tetrahydro-1H-imidazo[4,5-c]pyridine


Mass: 274.709 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.64 Å3/Da / Density % sol: 53.49 %

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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→45.36 Å / Num. obs: 28544 / % possible obs: 98.6 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.064 / Χ2: 0.97 / Net I/σ(I): 13 / Scaling rejects: 790
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.073.520.3563.1983827851.1196.8
2.07-2.153.630.3293.11019927931.1197.8
2.15-2.253.620.2693.81032028191.197.8
2.25-2.373.630.2054.81044928361.0698.1
2.37-2.523.630.15761044528200.9897.8
2.52-2.713.670.1178.11051628320.9398.5
2.71-2.993.690.07911.81062728670.9299.3
2.99-3.423.730.049181078628840.8599.7
3.42-4.313.730.0330.11094129270.8599.9
4.31-45.363.690.02338.11101229810.82100

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
REFMAC5.1.24refinement
PDB_EXTRACT3.005data extraction
RefinementResolution: 2→45.36 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.724 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1436 5 %RANDOM
Rwork0.2 ---
obs0.203 28538 98.55 %-
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: 34.176 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å2-0.52 Å2
2--0.32 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2763 0 20 143 2926
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0212857
X-RAY DIFFRACTIONr_bond_other_d0.0020.022544
X-RAY DIFFRACTIONr_angle_refined_deg1.661.9673856
X-RAY DIFFRACTIONr_angle_other_deg0.88635940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2125342
X-RAY DIFFRACTIONr_chiral_restr0.1020.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023177
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02626
X-RAY DIFFRACTIONr_nbd_refined0.2170.2580
X-RAY DIFFRACTIONr_nbd_other0.2450.22888
X-RAY DIFFRACTIONr_nbtor_other0.0880.21620
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2141
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.211
X-RAY DIFFRACTIONr_mcbond_it1.0531.51681
X-RAY DIFFRACTIONr_mcangle_it1.86122715
X-RAY DIFFRACTIONr_scbond_it2.53731176
X-RAY DIFFRACTIONr_scangle_it4.0074.51141
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.294 113
Rwork0.254 1937
all-2050

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