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- PDB-3nuu: phosphoinositide-dependent kinase-1 (PDK1) with fragment11 -

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Basic information

Entry
Database: PDB / ID: 3nuu
Titlephosphoinositide-dependent kinase-1 (PDK1) with fragment11
ComponentsPkB-like
KeywordsTRANSFERASE / Kinase domain
Function / homology
Function and homology information


intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process ...intracellular signaling cassette / Activation of AKT2 / regulation of mast cell degranulation / type B pancreatic cell development / negative regulation of toll-like receptor signaling pathway / RSK activation / regulation of canonical NF-kappaB signal transduction / hyperosmotic response / positive regulation of vascular endothelial cell proliferation / negative regulation of cardiac muscle cell apoptotic process / phospholipase activator activity / positive regulation of sprouting angiogenesis / Constitutive Signaling by AKT1 E17K in Cancer / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / negative regulation of endothelial cell apoptotic process / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / phospholipase binding / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / GPVI-mediated activation cascade / RHO GTPases activate PKNs / T cell costimulation / extrinsic apoptotic signaling pathway / Integrin signaling / insulin-like growth factor receptor signaling pathway / cellular response to epidermal growth factor stimulus / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / 3-phosphoinositide-dependent protein kinase activity / VEGFR2 mediated vascular permeability / cell projection / positive regulation of protein localization to plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of transforming growth factor beta receptor signaling pathway / calcium-mediated signaling / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / epidermal growth factor receptor signaling pathway / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / Downstream TCR signaling / G beta:gamma signalling through PI3Kgamma / insulin receptor signaling pathway / cell migration / PIP3 activates AKT signaling / protein autophosphorylation / actin cytoskeleton organization / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / postsynaptic density / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
PDK1-type, PH domain / PH domain / PDPK1 family / : / 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 ...PDK1-type, PH domain / PH domain / PDPK1 family / : / 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
3,4-dihydroisoquinolin-1(2H)-one / 3-phosphoinositide-dependent protein kinase 1 / non-specific serine/threonine protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9803 Å
AuthorsCampobasso, N. / Ward, P.
CitationJournal: ACS Med Chem Lett / Year: 2010
Title: Aminoindazole PDK1 Inhibitors: A Case Study in Fragment-Based Drug Discovery.
Authors: Medina, J.R. / Blackledge, C.W. / Heerding, D.A. / Campobasso, N. / Ward, P. / Briand, J. / Wright, L. / Axten, J.M.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _entity.formula_weight
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _struct_conn.pdbx_leaving_atom_flag / _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: PkB-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,63316
Polymers33,1571
Non-polymers1,47615
Water2,432135
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: PkB-like
hetero molecules

A: PkB-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,26732
Polymers66,3142
Non-polymers2,95230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area7540 Å2
ΔGint-302 kcal/mol
Surface area24380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.615, 122.615, 47.328
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-485-

HOH

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Components

#1: Protein PkB-like


Mass: 33157.141 Da / Num. of mol.: 1 / Fragment: UNP residues 65-350
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PkB-like 1 / Production host: Baculovirus / References: UniProt: Q9UPJ8, UniProt: O15530*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-JOZ / 3,4-dihydroisoquinolin-1(2H)-one


Mass: 147.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H9NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298 K / Method: sitting drop / pH: 9
Details: 2M Ammonium sulfate, 0.1M TRIS, pH 9, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.99 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 25044 / % possible obs: 87.2 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.099 / Χ2: 1.08 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.98-2.053.20.47312190.921142.8
2.05-2.134.30.44717490.964161.7
2.13-2.235.20.37121681.012176.1
2.23-2.356.20.34126121.024191.9
2.35-2.497.80.3228181.007198.6
2.49-2.6910.30.29628490.9821100
2.69-2.9611.10.18228570.9821100
2.96-3.3911.20.10728961.0091100
3.39-4.2611.20.06428941.4351100
4.26-5010.80.04129821.112199.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9803→37.4635 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8126 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.2387 1266 5.06 %
Rwork0.1888 --
obs-25023 45.16 %
Solvent computationBsol: 52.03 Å2 / ksol: 0.382 e/Å3
Displacement parametersBiso max: 144.75 Å2 / Biso mean: 31.1634 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-3.287 Å20 Å2-0 Å2
2--3.287 Å2-0 Å2
3----6.574 Å2
Refinement stepCycle: LAST / Resolution: 1.9803→37.4635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2243 0 85 135 2463
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d0.561
X-RAY DIFFRACTIONf_bond_d0.0031
X-RAY DIFFRACTIONf_chiral_restr0.0441
X-RAY DIFFRACTIONf_dihedral_angle_d9.3611
X-RAY DIFFRACTIONf_plane_restr0.0021
X-RAY DIFFRACTIONf_nbd_refined4.0831
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
1.9803-1.99420.2629192X-RAY DIFFRACTION4817
1.9942-2.00850.2777210X-RAY DIFFRACTION4818
2.0085-2.02330.2595227X-RAY DIFFRACTION4820
2.0233-2.03850.2505304X-RAY DIFFRACTION4825
2.0385-2.05420.25278X-RAY DIFFRACTION4824
2.0542-2.07040.2695301X-RAY DIFFRACTION4827
2.0704-2.08710.2566323X-RAY DIFFRACTION4827
2.0871-2.10430.2308345X-RAY DIFFRACTION4831
2.1043-2.12210.2548371X-RAY DIFFRACTION4832
2.1221-2.14060.2442385X-RAY DIFFRACTION4834
2.1406-2.15970.2605419X-RAY DIFFRACTION4835
2.1597-2.17950.2259410X-RAY DIFFRACTION4836
2.1795-2.20010.2246422X-RAY DIFFRACTION4837
2.2001-2.22140.2195468X-RAY DIFFRACTION4840
2.2214-2.24360.2328489X-RAY DIFFRACTION4843
2.2436-2.26680.2262520X-RAY DIFFRACTION4844
2.2668-2.29090.2211489X-RAY DIFFRACTION4845
2.2909-2.31610.2127531X-RAY DIFFRACTION4845
2.3161-2.34240.197548X-RAY DIFFRACTION4847
2.3424-2.36990.2166545X-RAY DIFFRACTION4848
2.3699-2.39880.2128544X-RAY DIFFRACTION4848
2.3988-2.42920.2076554X-RAY DIFFRACTION4849
2.4292-2.46110.1966571X-RAY DIFFRACTION4849
2.4611-2.49480.2079588X-RAY DIFFRACTION4849
2.4948-2.53050.1925549X-RAY DIFFRACTION4849
2.5305-2.56820.1946540X-RAY DIFFRACTION4848
2.5682-2.60840.2027560X-RAY DIFFRACTION4848
2.6084-2.65110.2045566X-RAY DIFFRACTION4849
2.6511-2.69680.189549X-RAY DIFFRACTION4848
2.6968-2.74580.1891585X-RAY DIFFRACTION4849
2.7458-2.79860.1825579X-RAY DIFFRACTION4850
2.7986-2.85570.1849552X-RAY DIFFRACTION4849
2.8557-2.91780.191560X-RAY DIFFRACTION4848
2.9178-2.98570.2148585X-RAY DIFFRACTION4850
2.9857-3.06030.1837549X-RAY DIFFRACTION4849
3.0603-3.1430.18566X-RAY DIFFRACTION4849
3.143-3.23540.1768572X-RAY DIFFRACTION4850
3.2354-3.33980.1727573X-RAY DIFFRACTION4850
3.3398-3.45910.1809584X-RAY DIFFRACTION4850
3.4591-3.59750.1702572X-RAY DIFFRACTION4849
3.5975-3.76110.1551572X-RAY DIFFRACTION4849
3.7611-3.95910.1422584X-RAY DIFFRACTION4850
3.9591-4.20690.1401546X-RAY DIFFRACTION4849
4.2069-4.53120.1396591X-RAY DIFFRACTION4850
4.5312-4.98630.156584X-RAY DIFFRACTION4851
4.9863-5.70560.1918596X-RAY DIFFRACTION4851
5.7056-7.18020.1923585X-RAY DIFFRACTION4851
7.1802-37.47020.1804624X-RAY DIFFRACTION4854

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