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- PDB-5lvl: Human PDK1 Kinase Domain in Complex with Compound PS653 Bound to ... -

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Basic information

Entry
Database: PDB / ID: 5lvl
TitleHuman PDK1 Kinase Domain in Complex with Compound PS653 Bound to the ATP-Binding Site
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE / protein kinase / allosteric regulation / small compounds / PIF-pocket
Function / homology
Function and homology information


3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / positive regulation of vascular endothelial cell proliferation ...3-phosphoinositide-dependent protein kinase activity / Activation of AKT2 / regulation of mast cell degranulation / negative regulation of toll-like receptor signaling pathway / type B pancreatic cell development / positive regulation of phospholipase activity / RSK activation / hyperosmotic response / regulation of canonical NF-kappaB signal transduction / 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 / phospholipase binding / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of endothelial cell apoptotic process / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / extrinsic apoptotic signaling pathway / RHO GTPases activate PKNs / cellular response to epidermal growth factor stimulus / GPVI-mediated activation cascade / T cell costimulation / activation of protein kinase B activity / Integrin signaling / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / peptidyl-threonine phosphorylation / negative regulation of transforming growth factor beta receptor signaling pathway / negative regulation of protein kinase activity / epidermal growth factor receptor signaling pathway / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / G beta:gamma signalling through PI3Kgamma / cellular response to insulin stimulus / positive regulation of angiogenesis / Regulation of TP53 Degradation / cell migration / Downstream TCR signaling / insulin receptor signaling pathway / PIP3 activates AKT signaling / cytoplasmic vesicle / actin cytoskeleton organization / protein autophosphorylation / postsynaptic density / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...PDK1-type, PH domain / PDPK1 family / PH domain / PH-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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
2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE / DITHIANE DIOL / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Suess, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. ...Schulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Suess, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. / Alzari, P.M. / Gervasio, F.L. / Biondi, R.M.
Funding support Germany, 3items
OrganizationGrant numberCountry
BMBF GO-Bio0315102 Germany
German Research FoundationBI 1044/2-3 Germany
German Research FoundationBI 1044/12-1 Germany
CitationJournal: Cell Chem Biol / Year: 2016
Title: Bidirectional Allosteric Communication between the ATP-Binding Site and the Regulatory PIF Pocket in PDK1 Protein Kinase.
Authors: Schulze, J.O. / Saladino, G. / Busschots, K. / Neimanis, S. / Su, E. / Odadzic, D. / Zeuzem, S. / Hindie, V. / Herbrand, A.K. / Lisa, M.N. / Alzari, P.M. / Gervasio, F.L. / Biondi, R.M.
History
DepositionSep 14, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2016Group: Database references
Revision 2.0Oct 16, 2019Group: Atomic model / Author supporting evidence / Data collection
Category: atom_site / pdbx_audit_support / reflns_shell
Item: _atom_site.occupancy / _pdbx_audit_support.funding_organization
Revision 2.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9996
Polymers35,3931
Non-polymers6075
Water4,810267
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint4 kcal/mol
Surface area14290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.240, 44.430, 47.250
Angle α, β, γ (deg.)90.00, 100.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-563-

HOH

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Components

#1: Protein 3-phosphoinositide-dependent protein kinase 1 / hPDK1


Mass: 35392.566 Da / Num. of mol.: 1 / Mutation: Y288G, Q292A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDPK1, PDK1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-537 / 2,6-DIHYDROANTHRA/1,9-CD/PYRAZOL-6-ONE


Mass: 220.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H8N2O / Comment: inhibitor*YM
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.2 M NA CITRATE, 0.1 M HEPES PH 7.5, 0.01 M DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.4→73 Å / Num. obs: 59735 / % possible obs: 99.8 % / Redundancy: 4 % / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HRC

3hrc


Resolution: 1.4→72.917 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 16.85
RfactorNum. reflection% reflection
Rfree0.178 2987 5 %
Rwork0.1529 --
obs0.1542 59735 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.4→72.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2325 0 37 267 2629
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132627
X-RAY DIFFRACTIONf_angle_d1.5663583
X-RAY DIFFRACTIONf_dihedral_angle_d12.6961042
X-RAY DIFFRACTIONf_chiral_restr0.094389
X-RAY DIFFRACTIONf_plane_restr0.01456
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3999-1.42290.2541390.25272652X-RAY DIFFRACTION100
1.4229-1.44740.28521430.24762713X-RAY DIFFRACTION100
1.4474-1.47370.22931420.23512695X-RAY DIFFRACTION100
1.4737-1.50210.25221400.21482652X-RAY DIFFRACTION100
1.5021-1.53270.21431420.20312714X-RAY DIFFRACTION100
1.5327-1.56610.22581390.18732634X-RAY DIFFRACTION100
1.5661-1.60250.19211430.17152712X-RAY DIFFRACTION100
1.6025-1.64260.20581420.16342706X-RAY DIFFRACTION100
1.6426-1.6870.18071420.15842702X-RAY DIFFRACTION100
1.687-1.73670.16941420.1472681X-RAY DIFFRACTION100
1.7367-1.79270.20431410.14772682X-RAY DIFFRACTION100
1.7927-1.85680.16581430.15062723X-RAY DIFFRACTION100
1.8568-1.93110.17751410.1412682X-RAY DIFFRACTION100
1.9311-2.0190.16731420.13472702X-RAY DIFFRACTION100
2.019-2.12550.15621420.12812695X-RAY DIFFRACTION100
2.1255-2.25870.161430.12582705X-RAY DIFFRACTION100
2.2587-2.43310.14641420.1272705X-RAY DIFFRACTION100
2.4331-2.67790.19751430.14572720X-RAY DIFFRACTION100
2.6779-3.06540.16481430.14722724X-RAY DIFFRACTION100
3.0654-3.86210.14961450.14332739X-RAY DIFFRACTION100
3.8621-73.01580.18491480.15912810X-RAY DIFFRACTION100
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)
15.3988-0.0083-0.34735.49660.00334.1140.10620.02810.60870.0849-0.1067-0.0495-0.36740.0198-0.01850.17790.0315-0.00880.29430.01750.1362-7.51382.8712-15.6099
23.2234-0.20760.98613.1669-0.42362.05060.0660.39030.1551-0.1796-0.09520.2581-0.2967-0.1786-0.0320.15530.06560.00130.27120.02480.1112-9.38883.5609-14.3848
34.9479-1.58642.21235.0766-2.88336.78250.4270.65290.2896-0.285-0.36860.1695-0.507-0.50410.00370.32830.12270.09070.39920.03470.3004-16.676212.4462-3.9551
41.88291.1553-1.15641.8972-1.05872.2445-0.09890.1868-0.0188-0.26160.0789-0.00680.0321-0.05930.0060.10810.02920.00360.1217-0.00670.098-13.8738-3.2847-5.1713
51.3321-0.04790.09331.8002-0.14461.0342-0.00790.02930.1496-0.0445-0.0127-0.0172-0.10340.03010.00890.0773-0.01050.00260.0830.0010.0785-21.65221.06056.2165
61.2923-0.26090.38221.9748-0.04111.35830.0293-0.1123-0.12310.05510.01150.21140.0821-0.137-0.02150.0815-0.01310.00590.10040.00730.1143-33.2475-7.034310.3743
72.9326-1.0832-0.79812.61290.58162.6245-0.0033-0.1078-0.2050.067-0.0205-0.17640.12230.1580.0320.11730.0021-0.02320.13270.03220.122-16.1489-10.912715.5227
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 74 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 120 )
3X-RAY DIFFRACTION3chain 'A' and (resid 121 through 136 )
4X-RAY DIFFRACTION4chain 'A' and (resid 137 through 178 )
5X-RAY DIFFRACTION5chain 'A' and (resid 179 through 260 )
6X-RAY DIFFRACTION6chain 'A' and (resid 261 through 327 )
7X-RAY DIFFRACTION7chain 'A' and (resid 328 through 359 )

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