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- PDB-5lvp: Human PDK1 Kinase Domain in Complex with an HM-Peptide Bound to t... -

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Basic information

Entry
Database: PDB / ID: 5lvp
TitleHuman PDK1 Kinase Domain in Complex with an HM-Peptide Bound to the PIF-Pocket
Components
  • 3-phosphoinositide-dependent protein kinase 1
  • hydrophobic-motif peptide of PKB/Akt
KeywordsTRANSFERASE / protein kinase / allosteric regulation / small compounds / PIF-pocket
Function / homology
Function and homology information


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 ...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 / phospholipase binding / CD28 dependent PI3K/Akt signaling / positive regulation of blood vessel endothelial cell migration / Role of LAT2/NTAL/LAB on calcium mobilization / Estrogen-stimulated signaling through PRKCZ / vascular endothelial cell response to laminar fluid shear stress / negative regulation of endothelial cell apoptotic process / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / activation of protein kinase B activity / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / GPVI-mediated activation cascade / extrinsic apoptotic signaling pathway / T cell costimulation / Integrin signaling / peptidyl-threonine phosphorylation / cellular response to epidermal growth factor stimulus / insulin-like growth factor receptor signaling pathway / positive regulation of release of sequestered calcium ion into cytosol / VEGFR2 mediated cell proliferation / 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 / epidermal growth factor receptor signaling pathway / FCERI mediated NF-kB activation / cellular response to insulin stimulus / positive regulation of angiogenesis / G beta:gamma signalling through PI3Kgamma / Regulation of TP53 Degradation / insulin receptor signaling pathway / Downstream TCR signaling / cell migration / PIP3 activates AKT signaling / actin cytoskeleton organization / protein autophosphorylation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / cytoplasmic vesicle / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / 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
ADENOSINE-5'-TRIPHOSPHATE / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 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 1.2Oct 16, 2019Group: Advisory / Author supporting evidence / Data collection
Category: pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms / reflns_shell
Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
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
B: 3-phosphoinositide-dependent protein kinase 1
C: 3-phosphoinositide-dependent protein kinase 1
D: 3-phosphoinositide-dependent protein kinase 1
E: hydrophobic-motif peptide of PKB/Akt
F: hydrophobic-motif peptide of PKB/Akt
G: hydrophobic-motif peptide of PKB/Akt
H: hydrophobic-motif peptide of PKB/Akt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,71614
Polymers147,6168
Non-polymers2,1006
Water5,152286
1
A: 3-phosphoinositide-dependent protein kinase 1
F: hydrophobic-motif peptide of PKB/Akt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4113
Polymers36,9042
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-phosphoinositide-dependent protein kinase 1
G: hydrophobic-motif peptide of PKB/Akt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4474
Polymers36,9042
Non-polymers5432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-phosphoinositide-dependent protein kinase 1
E: hydrophobic-motif peptide of PKB/Akt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4474
Polymers36,9042
Non-polymers5432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-phosphoinositide-dependent protein kinase 1
H: hydrophobic-motif peptide of PKB/Akt
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4113
Polymers36,9042
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.830, 168.510, 94.880
Angle α, β, γ (deg.)90.00, 93.06, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 35392.566 Da / Num. of mol.: 4 / 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: Protein/peptide
hydrophobic-motif peptide of PKB/Akt


Mass: 1511.509 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.59 Å3/Da / Density % sol: 52.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 1.65 M Ammonium Sulfate, 1 M Na Citrate pH 5.7, 0.01 M DTT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→95 Å / Num. obs: 51591 / % possible obs: 99.7 % / Redundancy: 4.2 % / Net I/σ(I): 12.5

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementResolution: 2.5→94.745 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 26.75
RfactorNum. reflection% reflection
Rfree0.2257 2575 5 %
Rwork0.1737 --
obs0.1764 51496 99.48 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Refinement stepCycle: LAST / Resolution: 2.5→94.745 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9126 0 126 286 9538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079481
X-RAY DIFFRACTIONf_angle_d0.9712847
X-RAY DIFFRACTIONf_dihedral_angle_d14.1485623
X-RAY DIFFRACTIONf_chiral_restr0.0561394
X-RAY DIFFRACTIONf_plane_restr0.0061601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.58940.3292510.26834771X-RAY DIFFRACTION97
2.5894-2.6930.30782590.23854912X-RAY DIFFRACTION100
2.693-2.81560.32662590.23534925X-RAY DIFFRACTION100
2.8156-2.96410.27232570.21444882X-RAY DIFFRACTION100
2.9641-3.14980.26812580.20484892X-RAY DIFFRACTION100
3.1498-3.3930.27172600.19784936X-RAY DIFFRACTION100
3.393-3.73450.21542570.15194890X-RAY DIFFRACTION100
3.7345-4.27480.16952580.1224911X-RAY DIFFRACTION100
4.2748-5.38580.16122600.12094923X-RAY DIFFRACTION100
5.3858-94.81310.19692560.18154879X-RAY DIFFRACTION98
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)
16.0540.2145-0.45833.3981-0.18994.14890.15140.66110.0857-0.2473-0.07020.3042-0.30990.1607-0.10070.27030.046-0.0420.40320.00130.325-31.543924.53-53.3638
23.06680.0131.36651.40490.09721.90160.080.0373-0.1418-0.08-0.05190.0577-0.1869-0.2208-0.00510.26520.07180.02430.32410.03290.2921-18.211626.6468-44.7734
32.87460.3463-0.14632.40170.45352.93570.07020.13030.31680.0059-0.0253-0.028-0.4458-0.05230.03670.29910.0504-0.00380.20610.06760.2773-4.727735.3537-39.835
43.98331.00640.13654.3211-4.97368.5496-0.22930.7178-0.0797-0.85760.1972-0.72841.1919-0.15870.01930.33910.07540.05560.3937-0.00970.5706-7.8288-0.3494-50.8902
54.36640.8123-1.0491.1881-0.76451.9746-0.02260.6624-0.0161-0.20610.0472-0.21640.34470.0931-0.07330.3350.0636-0.0250.3376-0.09210.3934-16.6378-3.1417-49.9662
63.80180.32910.30121.5895-0.62183.81170.02760.3280.1019-0.0919-0.0417-0.06680.17130.06870.02840.25690.0623-0.02640.2662-0.05640.2539-30.1885-5.9657-45.2113
72.66350.11941.08632.15220.32823.57950.32720.0203-0.39430.0906-0.16680.09590.6397-0.44470.04930.3913-0.0283-0.03550.2968-0.11080.3904-38.6322-13.7017-40.3551
83.15571.5036-0.66866.45634.01936.0953-0.1776-0.3693-0.23250.98360.23070.25711.03210.22080.09370.3150.0214-0.05050.36780.03630.4642-38.31950.1132.0215
93.1396-1.20050.67423.14370.04832.63130.138-0.38250.08490.1504-0.24220.3910.3793-0.13550.03620.2739-0.05220.08130.37440.08430.3789-36.151-0.1283.1114
103.4474-1.0746-1.7181.75310.47072.0268-0.0266-0.41630.00050.11830.15480.0550.3495-0.1482-0.17820.225-0.076-0.02630.35110.07450.2701-25.9425-2.80320.8287
113.6936-0.04490.62742.77560.65383.97250.026-0.2631-0.01120.0953-0.05080.1168-0.0355-0.2150.05190.2248-0.05250.00090.25140.07290.266-15.5409-5.1311-3.2283
122.889-0.27271.67292.6365-0.57114.16760.27810.1719-0.373-0.1545-0.1314-0.02840.39380.5476-0.01350.32280.0106-0.06040.32760.08620.404-7.1102-13.1491-7.7046
134.51-0.0234-0.60996.9813-3.30993.3972-0.0305-0.3728-0.08821.40830.3679-0.2242-1.2792-0.033-0.23230.4427-0.01890.06220.4150.02210.3748-9.625422.93662.4267
143.6269-1.67640.23812.70540.07363.41540.1402-0.57520.01770.2038-0.228-0.2487-0.52150.1339-0.00250.2729-0.120.01330.3651-0.04490.3183-11.465724.26673.1603
156.07720.23914.27934.24441.87224.49810.6933-1.77270.90370.5577-0.03880.0017-0.3094-0.4576-0.15290.506-0.10860.13760.8083-0.11740.3929-23.1629.334911.8599
164.1564-0.58762.19521.2464-0.81592.83750.24350.0388-0.06750.0398-0.1866-0.2483-0.12960.4844-0.04250.2391-0.04120.06760.3193-0.02680.3023-21.14725.5195-3.7009
172.2047-0.3833-0.36931.40170.18585.25830.0042-0.0995-0.04950.0571-0.0350.12380.26590.0590.00710.2399-0.03760.04610.2271-0.00910.2878-32.727726.9347-6.6423
180.7779-0.2160.27192.352-1.9641.65160.0779-0.70330.36030.9407-0.3172-0.1131-0.92280.42990.1670.6295-0.1201-0.08380.5483-0.19420.5741-33.482739.6564.6094
191.43060.0884-0.18911.56990.57472.00480.0045-0.0210.48920.0185-0.1027-0.2122-0.767-0.07090.10080.4092-0.02360.00270.2292-0.0650.4049-40.587941.6218-9.2066
205.6751-1.9258-2.04772.18811.29083.18990.05930.1612-0.71690.12-0.39220.1630.418-0.40870.29010.3142-0.0643-0.01230.3117-0.07410.3052-42.369823.2493-10.5202
217.28022.3781-5.49777.4919-4.48075.22520.6777-0.8207-0.65520.72721.19080.3687-0.15260.3611-1.01461.0624-0.2015-0.27991.13810.16010.5624-31.13111.943615.585
220.6364-0.8165-0.93674.55970.04031.76040.09350.9599-0.0358-1.2748-0.08820.45470.6718-0.3448-0.22840.9927-0.0969-0.08571.1589-0.05010.302-28.850321.0924-63.4148
235.2739-3.1386-1.82282.50493.01816.73380.98261.5374-0.2041-1.26870.218-0.5323-0.78970.1617-1.04610.9084-0.10390.1121.0512-0.15340.8215-14.90291.2735-63.5998
240.6570.20050.32924.23976.21559.23780.0604-1.220.02810.6340.3647-0.50970.73270.2062-0.12311.027-0.30680.07551.1036-0.02090.5265-16.51321.274815.0302
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 75 through 136 )
2X-RAY DIFFRACTION2chain 'A' and (resid 137 through 245 )
3X-RAY DIFFRACTION3chain 'A' and (resid 246 through 359 )
4X-RAY DIFFRACTION4chain 'B' and (resid 74 through 94 )
5X-RAY DIFFRACTION5chain 'B' and (resid 95 through 178 )
6X-RAY DIFFRACTION6chain 'B' and (resid 179 through 245 )
7X-RAY DIFFRACTION7chain 'B' and (resid 246 through 359 )
8X-RAY DIFFRACTION8chain 'C' and (resid 75 through 94 )
9X-RAY DIFFRACTION9chain 'C' and (resid 95 through 120 )
10X-RAY DIFFRACTION10chain 'C' and (resid 121 through 178 )
11X-RAY DIFFRACTION11chain 'C' and (resid 179 through 245 )
12X-RAY DIFFRACTION12chain 'C' and (resid 246 through 359 )
13X-RAY DIFFRACTION13chain 'D' and (resid 74 through 94 )
14X-RAY DIFFRACTION14chain 'D' and (resid 95 through 120 )
15X-RAY DIFFRACTION15chain 'D' and (resid 121 through 136 )
16X-RAY DIFFRACTION16chain 'D' and (resid 137 through 178 )
17X-RAY DIFFRACTION17chain 'D' and (resid 179 through 221 )
18X-RAY DIFFRACTION18chain 'D' and (resid 222 through 260 )
19X-RAY DIFFRACTION19chain 'D' and (resid 261 through 327 )
20X-RAY DIFFRACTION20chain 'D' and (resid 328 through 359 )
21X-RAY DIFFRACTION21chain 'E' and (resid 8 through 14 )
22X-RAY DIFFRACTION22chain 'F' and (resid 8 through 15 )
23X-RAY DIFFRACTION23chain 'G' and (resid 8 through 15 )
24X-RAY DIFFRACTION24chain 'H' and (resid 8 through 14 )

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