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- PDB-2x18: The crystal structure of the PH domain of human AKT3 protein kinase -

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Basic information

Entry
Database: PDB / ID: 2x18
TitleThe crystal structure of the PH domain of human AKT3 protein kinase
ComponentsRAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
KeywordsTRANSFERASE / KINASE / MEMBRANE / ATP-BINDING
Function / homology
Function and homology information


positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / : / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of cell migration involved in sprouting angiogenesis ...positive regulation of artery morphogenesis / AKT-mediated inactivation of FOXO1A / Negative regulation of the PI3K/AKT network / AKT phosphorylates targets in the nucleus / RUNX2 regulates genes involved in cell migration / : / RAB GEFs exchange GTP for GDP on RABs / brain morphogenesis / AKT phosphorylates targets in the cytosol / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of vascular endothelial cell proliferation / Regulation of TP53 Activity through Association with Co-factors / Co-inhibition by CTLA4 / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of PERK-mediated unfolded protein response / negative regulation of cellular senescence / Regulation of localization of FOXO transcription factors / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Estrogen-dependent nuclear events downstream of ESR-membrane signaling / positive regulation of cell size / Activation of BAD and translocation to mitochondria / positive regulation of TOR signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Regulation of TP53 Activity through Acetylation / positive regulation of endothelial cell proliferation / FLT3 Signaling / Transcriptional and post-translational regulation of MITF-M expression and activity / homeostasis of number of cells within a tissue / Downregulation of ERBB2:ERBB3 signaling / VEGFR2 mediated vascular permeability / TP53 Regulates Metabolic Genes / Regulation of PTEN stability and activity / positive regulation of angiogenesis / KEAP1-NFE2L2 pathway / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / PIP3 activates AKT signaling / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / cilium / ciliary basal body / protein serine kinase activity / protein serine/threonine kinase activity / Golgi apparatus / signal transduction / nucleoplasm / ATP binding / plasma membrane / cytosol
Similarity search - Function
Protein kinase B gamma, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / PH domain ...Protein kinase B gamma, catalytic domain / Protein Kinase B, pleckstrin homology domain / Protein kinase, C-terminal / Protein kinase C terminal domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / 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 / Roll / 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 / Mainly Beta
Similarity search - Domain/homology
RAC-gamma serine/threonine-protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsVollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. ...Vollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: The Crystal Structure of the Ph Domain of Human Akt3 Protein Kinase
Authors: Vollmar, M. / Wang, J. / Zhang, Y. / Elkins, J.M. / Burgess-Brown, N. / Chaikuad, A. / Pike, A.C.W. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
History
DepositionDec 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
B: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
C: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
D: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
E: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
F: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
G: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
H: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,25912
Polymers114,3068
Non-polymers9534
Water30,9321717
1
A: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE


Theoretical massNumber of molelcules
Total (without water)14,2881
Polymers14,2881
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5272
Polymers14,2881
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.475, 62.401, 71.411
Angle α, β, γ (deg.)111.47, 102.75, 94.36
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
RAC-GAMMA SERINE/THREONINE-PROTEIN KINASE / RAC-PK-GAMMA / PROTEIN KINASE AKT-3 / PROTEIN KINASE B GAMMA / PKB GAMMA / STK-2 / AKT3


Mass: 14288.233 Da / Num. of mol.: 8 / Fragment: PH DOMAIN, RESIDUES 466-583
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: Q9Y243, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1717 / Source method: isolated from a natural source / Formula: H2O

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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: 2.45 Å3/Da / Density % sol: 49.81 % / Description: NONE
Crystal growDetails: 0.2M PROLINE, 0.1M HEPES PH 7.5, 10% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 21, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.46→64.03 Å / Num. obs: 164858 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 15.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10
Reflection shellResolution: 1.46→1.54 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2 / % possible all: 94.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0089refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UNP

1unp


Resolution: 1.46→64.03 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.003 / SU ML: 0.052 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.23377 8269 5 %RANDOM
Rwork0.18934 ---
obs0.19156 156074 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.825 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å2-0.22 Å2-0.22 Å2
2---0.35 Å20.01 Å2
3---0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.46→64.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7506 0 28 1717 9251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227910
X-RAY DIFFRACTIONr_bond_other_d0.0010.025514
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9510741
X-RAY DIFFRACTIONr_angle_other_deg2.369313469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.365925
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.62224.03402
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.619151440
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9651568
X-RAY DIFFRACTIONr_chiral_restr0.1190.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218643
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021619
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.55734651
X-RAY DIFFRACTIONr_mcbond_other0.8331816
X-RAY DIFFRACTIONr_mcangle_it3.83557621
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.1983259
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.652113108
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.369 578 -
Rwork0.341 11046 -
obs--93.74 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08030.3079-0.13770.69910.07350.542-0.0024-0.0904-0.02460.06890.00290.02070.02650.0325-0.00050.00960.00760.00270.02010.00230.002328.760892.472614.85
20.46060.19250.24860.6275-0.13810.825-0.0065-0.05870.0270.09190.030.0190.0379-0.0527-0.02350.02850.0107-0.00290.0298-0.00570.007462.884760.605115.1801
30.60860.2911-0.08170.37330.15890.96070.0412-0.06690.02130.0492-0.02180.0348-0.00130.0031-0.01940.00830.0010.00450.0207-0.0050.007660.781692.03415.0711
40.47330.2424-0.06620.65080.40370.92030.00630.06110.0092-0.070.01260.0291-0.05520.0144-0.01890.01850.0067-0.00680.013-0.00170.008426.070887.9741-12.8494
50.72590.56410.0140.9313-0.14970.20750.0541-0.0526-0.030.1145-0.09570.051-0.02410.06240.04160.0164-0.00690.0070.04170.0090.041230.339260.563515.4946
60.58820.20870.02621.2788-0.04770.55270.00530.04880.0114-0.0915-0.01560.00020.0120.00880.01030.01230.0063-0.00150.00750.00070.003458.271857.5491-12.7165
70.47130.19120.06320.57590.01740.9694-0.01170.04790.0288-0.06580.01970.03230.0018-0.008-0.00810.01380.0027-0.00660.00810.00180.006357.399888.1157-12.8178
80.62230.4032-0.20441.0052-0.04910.4241-0.04170.06820.0114-0.07120.0265-0.02970.04150.00720.01520.01870.0032-0.00390.01210.00150.009527.917958.5649-13.5134
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 114
2X-RAY DIFFRACTION2B4 - 117
3X-RAY DIFFRACTION3C4 - 118
4X-RAY DIFFRACTION4D4 - 118
5X-RAY DIFFRACTION5E3 - 118
6X-RAY DIFFRACTION6F3 - 113
7X-RAY DIFFRACTION7G4 - 118
8X-RAY DIFFRACTION8H3 - 118

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