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- PDB-3orx: PDK1 mutant bound to allosteric disulfide fragment inhibitor 1F8 -

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Basic information

Entry
Database: PDB / ID: 3orx
TitlePDK1 mutant bound to allosteric disulfide fragment inhibitor 1F8
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PIF pocket / C-helix / activation loop / AGC kinase / Transferase / Allosteric inhibitor / Phosphorylation / allostery / disulfide / kinase / PDK1 / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / negative regulation of cardiac muscle cell apoptotic process ...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 / negative regulation of cardiac muscle cell apoptotic process / positive regulation of vascular endothelial cell proliferation / 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 / 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 / positive regulation of release of sequestered calcium ion into cytosol / insulin-like growth factor receptor signaling pathway / VEGFR2 mediated vascular permeability / VEGFR2 mediated cell proliferation / cell projection / calcium-mediated signaling / positive regulation of protein localization to plasma membrane / negative regulation of transforming growth factor beta receptor signaling pathway / peptidyl-threonine phosphorylation / 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 / cell migration / Regulation of TP53 Degradation / Downstream TCR signaling / PIP3 activates AKT signaling / insulin receptor signaling pathway / cytoplasmic vesicle / actin cytoskeleton organization / postsynaptic density / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / non-specific serine/threonine protein kinase / intracellular signal transduction / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Chem-1F8 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2044 Å
AuthorsSadowsky, J.D. / Wells, J.A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Turning a protein kinase on or off from a single allosteric site via disulfide trapping.
Authors: Sadowsky, J.D. / Burlingame, M.A. / Wolan, D.W. / McClendon, C.L. / Jacobson, M.P. / Wells, J.A.
History
DepositionSep 8, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ref_seq_dif.details / _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: 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: 3-phosphoinositide-dependent protein kinase 1
F: 3-phosphoinositide-dependent protein kinase 1
G: 3-phosphoinositide-dependent protein kinase 1
H: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,44420
Polymers289,4208
Non-polymers2,02412
Water23,3111294
1
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4483
Polymers36,1771
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4483
Polymers36,1771
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4483
Polymers36,1771
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4483
Polymers36,1771
Non-polymers2712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,1771
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,1771
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,1771
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4132
Polymers36,1771
Non-polymers2351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.289, 115.870, 145.718
Angle α, β, γ (deg.)91.76, 89.99, 95.41
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 75:236 or resseq 238:359 )
211chain B and (resseq 77:236 or resseq 239:359 )
311chain C and (resseq 75:236 or resseq 238:359 )
411chain D and (resseq 76:236 or resseq 238:359 )
112chain E and (resseq 76:231 or resseq 242:359 )
212chain F and (resseq 75:230 or resseq 241:359 )
312chain G and (resseq 75:230 or resseq 241:359 )
412chain H and (resseq 75:230 or resseq 241:359 )

NCS ensembles :
ID
1
2

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Components

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


Mass: 36177.457 Da / Num. of mol.: 8 / Fragment: Catalytic domain (UNP residues 51-359) / Mutation: T148C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PDK1, PDPK1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF21
References: UniProt: O15530, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-1F8 / 2-methyl-N-(2-sulfanylethyl)-1-benzofuran-3-carboxamide


Mass: 235.302 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C12H13NO2S
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1294 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2M lithium sulfate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11589 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11589 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 128125 / Num. obs: 128125 / % possible obs: 97.2 % / Redundancy: 1.8 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 12.765
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 2.761 / Num. unique all: 12662 / Rsym value: 0.303 / % possible all: 96.2

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Processing

Software
NameVersionClassification
CCP4model building
PHENIX(phenix.refine: 2010_01_09_2330)refinement
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1W

1h1w


Resolution: 2.2044→45.247 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2426 6442 5.03 %RANDOM
Rwork0.2076 ---
obs0.2094 128055 96.77 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.482 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.2571 Å20.0389 Å20.2399 Å2
2--1.5604 Å2-0.5387 Å2
3----1.5487 Å2
Refinement stepCycle: LAST / Resolution: 2.2044→45.247 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17617 0 132 1294 19043
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01318196
X-RAY DIFFRACTIONf_angle_d1.36224661
X-RAY DIFFRACTIONf_dihedral_angle_d19.8276487
X-RAY DIFFRACTIONf_chiral_restr0.0992708
X-RAY DIFFRACTIONf_plane_restr0.0063125
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2253X-RAY DIFFRACTIONPOSITIONAL
12B2253X-RAY DIFFRACTIONPOSITIONAL0.086
13C2251X-RAY DIFFRACTIONPOSITIONAL0.086
14D2251X-RAY DIFFRACTIONPOSITIONAL0.09
21E2102X-RAY DIFFRACTIONPOSITIONAL
22F2102X-RAY DIFFRACTIONPOSITIONAL0.186
23G2123X-RAY DIFFRACTIONPOSITIONAL0.166
24H2106X-RAY DIFFRACTIONPOSITIONAL0.17
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2044-2.22940.32861830.28163532X-RAY DIFFRACTION84
2.2294-2.25570.29542350.26393987X-RAY DIFFRACTION96
2.2557-2.28320.30072300.25283972X-RAY DIFFRACTION97
2.2832-2.31210.28792130.24684034X-RAY DIFFRACTION96
2.3121-2.34250.29552180.22844064X-RAY DIFFRACTION96
2.3425-2.37460.26882150.23264100X-RAY DIFFRACTION96
2.3746-2.40850.30082260.23053991X-RAY DIFFRACTION98
2.4085-2.44440.25952130.22134018X-RAY DIFFRACTION97
2.4444-2.48260.25262020.21534120X-RAY DIFFRACTION96
2.4826-2.52330.28682290.22584104X-RAY DIFFRACTION96
2.5233-2.56680.2872060.2223986X-RAY DIFFRACTION98
2.5668-2.61350.25982140.22524067X-RAY DIFFRACTION97
2.6135-2.66380.27342190.21514075X-RAY DIFFRACTION97
2.6638-2.71810.26252130.22174059X-RAY DIFFRACTION97
2.7181-2.77720.24591900.21544079X-RAY DIFFRACTION98
2.7772-2.84180.28721930.22124145X-RAY DIFFRACTION97
2.8418-2.91290.26912180.2174133X-RAY DIFFRACTION97
2.9129-2.99160.24292280.22193963X-RAY DIFFRACTION98
2.9916-3.07960.28252060.2294187X-RAY DIFFRACTION97
3.0796-3.1790.25962390.21534005X-RAY DIFFRACTION98
3.179-3.29260.24022070.20674120X-RAY DIFFRACTION98
3.2926-3.42440.22951940.19764161X-RAY DIFFRACTION98
3.4244-3.58020.19052290.18014063X-RAY DIFFRACTION98
3.5802-3.76890.19532280.17474108X-RAY DIFFRACTION98
3.7689-4.00480.19912240.17294108X-RAY DIFFRACTION97
4.0048-4.31380.21482140.18094087X-RAY DIFFRACTION98
4.3138-4.74750.22211930.17034117X-RAY DIFFRACTION98
4.7475-5.43350.19512040.18544036X-RAY DIFFRACTION96
5.4335-6.84190.22662220.21144156X-RAY DIFFRACTION99
6.8419-45.25610.23692370.21264036X-RAY DIFFRACTION97

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