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- PDB-1szm: DUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA) -

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Basic information

Entry
Database: PDB / ID: 1szm
TitleDUAL BINDING MODE OF BISINDOLYLMALEIMIDE 2 TO PROTEIN KINASE A (PKA)
ComponentscAMP-dependent protein kinase, alpha-catalytic subunitCAMP-dependent pathway
KeywordsTRANSFERASE / PKA / PKC / bisindolyl maleimide 2 / LY333531 / selectivity / surrogate kinase / amino acid residue exchange
Function / homology
Function and homology information


CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production ...CD209 (DC-SIGN) signaling / HDL assembly / Regulation of insulin secretion / Rap1 signalling / Ion homeostasis / PKA activation in glucagon signalling / DARPP-32 events / CREB1 phosphorylation through the activation of Adenylate Cyclase / GPER1 signaling / Factors involved in megakaryocyte development and platelet production / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / RET signaling / Interleukin-3, Interleukin-5 and GM-CSF signaling / Recruitment of NuMA to mitotic centrosomes / VEGFA-VEGFR2 Pathway / PKA activation / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / cAMP-dependent protein kinase / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / cAMP-dependent protein kinase activity / cAMP-dependent protein kinase complex / Vasopressin regulates renal water homeostasis via Aquaporins / AMP-activated protein kinase activity / protein kinase A regulatory subunit binding / mesoderm formation / sperm flagellum / protein kinase A signaling / negative regulation of TORC1 signaling / acrosomal vesicle / neuromuscular junction / cellular response to heat / peptidyl-serine phosphorylation / protein kinase activity / protein domain specific binding / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / perinuclear region of cytoplasm / mitochondrion / ATP binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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. ...cAMP-dependent protein kinase catalytic subunit / Extension to Ser/Thr-type protein kinases / AGC-kinase, C-terminal / AGC-kinase C-terminal domain profile. / 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-BI4 / cAMP-dependent protein kinase catalytic subunit alpha
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGassel, M. / Breitenlechner, C.B. / Koenig, N. / Huber, R. / Engh, R.A. / Bossemeyer, D.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The protein kinase C inhibitor bisindolyl maleimide 2 binds with reversed orientations to different conformations of protein kinase a.
Authors: Gassel, M. / Breitenlechner, C.B. / Koenig, N. / Huber, R. / Engh, R.A. / Bossemeyer, D.
#1: Journal: Structure / Year: 1997
Title: Staurosporine-induced conformational changes of cAMP-dependent protein kinase catalytic subunit explain inhibitory potential.
Authors: Prade, L. / Engh, R.A. / Girod, A. / Kinzel, V. / Huber, R. / Bossemeyer, D.
History
DepositionApr 6, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 1, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 600HETEROGEN Atom names used for BIM2 in this entry were chosen to comply with PDB ENTRY 1UU3. They ...HETEROGEN Atom names used for BIM2 in this entry were chosen to comply with PDB ENTRY 1UU3. They correspond to atom names used in the original CITATION AND REFERENCE 1 in the following manner: CAA=C3, CAB=C2, CAC=C1, CAD=C23, CAE=C5, CAF=C4, CAG=C22, NAH=N6, CAI=C21, CAJ=C17, CAK=C16, CAL=C8, CAM=C15, CAN=C10, NAO=N9, CAP=C14, CAQ=C13, CAR=C12, CAS=C11, CAT=C20, NAU=N19, CAV=C18, CAW=C7, OAX=O32, CAY=C24 , OAZ=O33, CBA=C25, CBB=C26, NBC=N30, CBD=C31, CBE=C27, CBF=C28, CBG=C29,

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: cAMP-dependent protein kinase, alpha-catalytic subunit
B: cAMP-dependent protein kinase, alpha-catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,4324
Polymers81,5552
Non-polymers8772
Water1,42379
1
A: cAMP-dependent protein kinase, alpha-catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2162
Polymers40,7771
Non-polymers4391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cAMP-dependent protein kinase, alpha-catalytic subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2162
Polymers40,7771
Non-polymers4391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.065, 89.005, 116.388
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein cAMP-dependent protein kinase, alpha-catalytic subunit / CAMP-dependent pathway / PKA C-alpha / PROTEIN KINASE A


Mass: 40777.426 Da / Num. of mol.: 2 / Mutation: V123A, L173M, Q181K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: PRKACA / Plasmid: pT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P00517, EC: 2.7.1.37
#2: 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.: 2 / Source method: obtained synthetically / Formula: C27H26N4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 79 / 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: 2.85 Å3/Da / Density % sol: 56.5 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6.4
Details: LiCl, MesBisTris, methanol, MEGA-8, PKI(5-24), pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2002 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→24.7 Å / Num. all: 31110 / Num. obs: 30100 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Rsym value: 0.099 / Net I/σ(I): 5.2
Reflection shellResolution: 2.5→2.64 Å / % possible obs: 99.9 % / Redundancy: 5 % / Mean I/σ(I) obs: 1 / Rsym value: 0.571 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4(MOLREP)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1STC
Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.893 / SU B: 11.441 / SU ML: 0.257 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.505 / ESU R Free: 0.318 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.289 1524 5.1 %RANDOM
Rwork0.231 ---
all0.234 28506 --
obs0.234 28506 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 47.536 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---2.57 Å20 Å2
3---1.71 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5181 0 66 79 5326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0215391
X-RAY DIFFRACTIONr_bond_other_d0.0020.024785
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9637309
X-RAY DIFFRACTIONr_angle_other_deg0.885311082
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7865638
X-RAY DIFFRACTIONr_chiral_restr0.0910.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025941
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021144
X-RAY DIFFRACTIONr_nbd_refined0.2090.21129
X-RAY DIFFRACTIONr_nbd_other0.230.25439
X-RAY DIFFRACTIONr_nbtor_other0.0890.23069
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2109
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2720.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.27
X-RAY DIFFRACTIONr_mcbond_it0.731.53191
X-RAY DIFFRACTIONr_mcangle_it1.36425116
X-RAY DIFFRACTIONr_scbond_it1.88432200
X-RAY DIFFRACTIONr_scangle_it3.0694.52193
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.383 115
Rwork0.317 2047

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