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- PDB-4a07: Human PDK1 Kinase Domain in Complex with Allosteric Activator PS1... -

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Basic information

Entry
Database: PDB / ID: 4a07
TitleHuman PDK1 Kinase Domain in Complex with Allosteric Activator PS171 Bound to the PIF-Pocket
Components3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1
KeywordsTRANSFERASE / ALLOSTERIC SITE
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
ADENOSINE-5'-TRIPHOSPHATE / Chem-AZ7 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSchulze, J.O. / Lopez-Garcia, L.A. / Froehner, W. / Zhang, H. / Navratil, J. / Hindie, V. / Zeuzem, S. / Alzari, P.M. / Neimanis, S. / Engel, M. / Biondi, R.M.
CitationJournal: Chem.Biol. / Year: 2011
Title: Allosteric Regulation of Protein Kinase Pkczeta by the N-Terminal C1 Domain and Small Compounds to the Pif-Pocket.
Authors: Lopez-Garcia, L.A. / Schulze, J.O. / Frohner, W. / Zhang, H. / Suss, E. / Weber, N. / Navratil, J. / Amon, S. / Hindie, V. / Zeuzem, S. / Jorgensen, T.J. / Alzari, P.M. / Neimanis, S. / Engel, M. / Biondi, R.M.
History
DepositionSep 8, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2011Group: Other
Revision 1.2Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)36,90110
Polymers35,4251
Non-polymers1,4769
Water3,765209
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)148.210, 44.030, 47.670
Angle α, β, γ (deg.)90.00, 101.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1 / HPDK1


Mass: 35424.629 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 50-359 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: O15530, non-specific serine/threonine protein kinase

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Non-polymers , 5 types, 218 molecules

#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-AZ7 / (3S)-3-(4-CHLOROPHENYL)-4-(5,7-DICHLORO-1H-BENZIMIDAZOL-2-YL)BUTANOIC ACID


Mass: 383.656 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H13Cl3N2O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 209 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, GLN 288 TO ALA ENGINEERED RESIDUE IN CHAIN A, TYR 292 TO GLY
Nonpolymer detailsPS171 (AZ7): ALLOSTERIC ACTIVATOR PS171

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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: 2.3 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 7.5 / Details: 1.2 M NA CITRATE 0.1 M HEPES PH 7.5 10 M DTT.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.9999
DetectorType: RAYONIX / Detector: CCD / Date: Dec 4, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.85→47 Å / Num. obs: 25852 / % possible obs: 99.3 % / Observed criterion σ(I): 2.8 / Redundancy: 4.6 % / Biso Wilson estimate: 16.59 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.8 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HRC

3hrc


Resolution: 1.85→36.242 Å / SU ML: 0.19 / σ(F): 2 / Phase error: 18.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1997 1292 5 %
Rwork0.1588 --
obs0.1609 25850 99.37 %
Solvent computationShrinkage radii: 0.89 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.291 Å2 / ksol: 0.426 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.5851 Å20 Å2-1.4489 Å2
2--0.2149 Å20 Å2
3---0.3702 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2240 0 85 209 2534
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082417
X-RAY DIFFRACTIONf_angle_d1.093308
X-RAY DIFFRACTIONf_dihedral_angle_d13.644884
X-RAY DIFFRACTIONf_chiral_restr0.074356
X-RAY DIFFRACTIONf_plane_restr0.005409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8499-1.9240.27681410.22612670X-RAY DIFFRACTION99
1.924-2.01150.2161410.18332692X-RAY DIFFRACTION99
2.0115-2.11760.23331420.15652692X-RAY DIFFRACTION99
2.1176-2.25020.17991430.14672717X-RAY DIFFRACTION99
2.2502-2.42390.18451430.14322722X-RAY DIFFRACTION99
2.4239-2.66780.20381440.15442740X-RAY DIFFRACTION100
2.6678-3.05360.21931440.15872723X-RAY DIFFRACTION100
3.0536-3.84660.17761450.15342762X-RAY DIFFRACTION100
3.8466-36.24860.18831490.15562840X-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)
12.29462.17820.39193.07990.24111.25320.12670.16560.2069-0.1657-0.13220.30110.0217-0.2107-0.01080.10350.0301-0.01860.210.03830.104-8.915524.5124-16.1908
20.1087-0.0676-0.24820.26670.64241.74990.00380.1490.0186-0.0325-0.0548-0.0423-0.11620.16320.06490.06790.0353-0.00780.20260.0330.0451-7.093325.6663-13.9567
32.7577-0.82620.31220.70960.49081.20120.46340.2953-0.072-0.1464-0.31110.1598-0.1858-0.3181-0.10380.18360.07080.01530.23650.01690.1795-16.300934.6489-4.4123
40.2466-0.03760.23950.8801-0.14311.8736-0.02940.03820.1257-0.0345-0.0186-0.0981-0.3676-0.04020.03180.1305-0.01760.00660.12740.02460.0846-7.356826.4935-3.8426
50.1774-0.2215-0.11411.6271-0.27070.31560.10540.07840.1141-0.1855-0.2508-0.0112-0.02510.080.10820.12430.0286-0.00290.15020.02020.0818-10.186324.5599-11.3339
60.91270.27920.10130.62440.36430.7323-0.05360.0098-0.11060.03860.0786-0.06610.04740.0707-0.04550.06870.0022-0.00460.0762-0.00880.086-19.903314.88095.681
71.0562-0.7376-0.36021.4892-0.09780.867-0.01610.08270.1239-0.04450.0051-0.24-0.16530.07020.02570.089-0.0239-0.0120.12330.00010.0835-17.003425.13924.0766
80.84480.0684-0.09520.2345-0.03410.6407-0.0518-0.01930.1327-0.02040.01490.1823-0.13570.04140.04080.09090.0053-0.02250.06450.00860.1002-30.792122.60656.5538
90.8385-0.180.25141.0455-0.14790.8777-0.0333-0.1049-0.12360.09760.010.24320.106-0.0920.01560.0895-0.00880.02670.07380.00530.1253-35.177915.5211.3834
100.59060.3334-0.12861.7423-0.64380.27230.1264-0.11550.06880.4545-0.1383-0.046-0.20710.13770.03720.18170.0111-0.05280.1537-0.00220.046-21.516222.232621.2906
110.8660.2832-0.5420.8243-0.13122.1632-0.3661-0.0517-0.42560.13170.0964-0.33490.44860.28680.14760.17380.0407-0.00080.16750.01750.1966-13.12278.963314.279
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 75:99)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 100:117)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 118:138)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 139:151)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 152:165)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 166:208)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 209:238)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 239:283)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 284:325)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 326:338)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 339:357)

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