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- PDB-3orz: PDK1 mutant bound to allosteric disulfide fragment activator 2A2 -

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Basic information

Entry
Database: PDB / ID: 3orz
TitlePDK1 mutant bound to allosteric disulfide fragment activator 2A2
Components3-phosphoinositide-dependent protein kinase 1
KeywordsTRANSFERASE/TRANSFERASE ACTIVATOR / C helix / Ser/Thr-kinase / AGC kinase / allostery / transferase / allosteric activator / bisindolylmaleimide / disulfide / kinase / PDK1 / TRANSFERASE-TRANSFERASE ACTIVATOR complex
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 / Estrogen-stimulated signaling through PRKCZ / negative regulation of endothelial cell apoptotic process / 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 / RHO GTPases activate PKNs / GPVI-mediated activation cascade / 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 / 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 / 3-phosphoinositide-dependent protein kinase activity / CLEC7A (Dectin-1) signaling / FCERI mediated NF-kB activation / cellular response to insulin stimulus / epidermal growth factor receptor signaling pathway / 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 / cytoplasmic vesicle / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / non-specific serine/threonine protein kinase / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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
Chem-2A2 / Chem-BI4 / 3-phosphoinositide-dependent protein kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9995 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
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,65912
Polymers144,7104
Non-polymers2,9498
Water14,574809
1
A: 3-phosphoinositide-dependent protein kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9153
Polymers36,1771
Non-polymers7372
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)36,9153
Polymers36,1771
Non-polymers7372
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)36,9153
Polymers36,1771
Non-polymers7372
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)36,9153
Polymers36,1771
Non-polymers7372
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)243.134, 116.124, 37.702
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 36177.457 Da / Num. of mol.: 4 / 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-2A2 / 4-[4-(3-chlorophenyl)piperazin-1-yl]-4-oxobutane-1-thiol


Mass: 298.831 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H19ClN2OS
#3: Chemical
ChemComp-BI4 / 3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE


Mass: 438.521 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H26N4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 809 / 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: 1.84 Å3/Da / Density % sol: 33.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 1.8M ammonium sulfate, 0.1M potassium tartrate, 0.1M sodium citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11588 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11588 Å / Relative weight: 1
ReflectionResolution: 1.999→50 Å / Num. all: 69773 / Num. obs: 69773 / % possible obs: 99.4 % / Redundancy: 3.7 % / Biso Wilson estimate: 19.65 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 20.456
Reflection shellResolution: 1.999→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.784 / Num. unique all: 3432 / Rsym value: 0.273 / % possible all: 99.9

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Processing

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

1h1w


Resolution: 1.9995→41.985 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 46.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2651 3505 5.05 %RANDOM
Rwork0.2178 ---
obs0.2203 69395 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.493 Å2 / ksol: 0.383 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.9995→41.985 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8954 0 208 809 9971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0099414
X-RAY DIFFRACTIONf_angle_d1.61812744
X-RAY DIFFRACTIONf_dihedral_angle_d20.093450
X-RAY DIFFRACTIONf_chiral_restr0.0871365
X-RAY DIFFRACTIONf_plane_restr0.0051600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9995-2.02690.34611110.32842239X-RAY DIFFRACTION85
2.0269-2.05580.33211420.3122639X-RAY DIFFRACTION100
2.0558-2.08650.35311470.29662754X-RAY DIFFRACTION100
2.0865-2.11910.2981300.2912612X-RAY DIFFRACTION100
2.1191-2.15380.34291500.27362641X-RAY DIFFRACTION100
2.1538-2.1910.311370.2642676X-RAY DIFFRACTION100
2.191-2.23080.26211480.25922706X-RAY DIFFRACTION100
2.2308-2.27370.32791280.25092624X-RAY DIFFRACTION100
2.2737-2.32010.2841300.24052692X-RAY DIFFRACTION100
2.3201-2.37060.30161530.23342701X-RAY DIFFRACTION100
2.3706-2.42570.2881470.24372613X-RAY DIFFRACTION100
2.4257-2.48640.26811380.22812689X-RAY DIFFRACTION100
2.4864-2.55360.30041360.22582681X-RAY DIFFRACTION100
2.5536-2.62870.26391500.21592651X-RAY DIFFRACTION100
2.6287-2.71360.2381420.22242713X-RAY DIFFRACTION100
2.7136-2.81050.31581310.2062638X-RAY DIFFRACTION100
2.8105-2.9230.27341530.21222702X-RAY DIFFRACTION100
2.923-3.0560.26471220.19272659X-RAY DIFFRACTION100
3.056-3.21710.2561490.18732695X-RAY DIFFRACTION100
3.2171-3.41860.25861430.1922667X-RAY DIFFRACTION99
3.4186-3.68240.20751650.17722602X-RAY DIFFRACTION99
3.6824-4.05270.2041380.17472594X-RAY DIFFRACTION97
4.0527-4.63840.24711220.16332647X-RAY DIFFRACTION97
4.6384-5.84140.22991500.19472626X-RAY DIFFRACTION98
5.8414-41.99440.2151430.21412429X-RAY DIFFRACTION89

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