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- PDB-7oal: Crystal structure of pseudokinase CASK in complex with compound 25 -

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Basic information

Entry
Database: PDB / ID: 7oal
TitleCrystal structure of pseudokinase CASK in complex with compound 25
ComponentsPeripheral plasma membrane protein CASK
KeywordsTRANSFERASE / pseudokinase / kinase / inhibitor / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors ...negative regulation of cellular response to growth factor stimulus / GMP kinase activity / neurexin family protein binding / Dopamine Neurotransmitter Release Cycle / negative regulation of wound healing / regulation of neurotransmitter secretion / nuclear lamina / calcium ion import / Nephrin family interactions / Assembly and cell surface presentation of NMDA receptors / Sensory processing of sound by outer hair cells of the cochlea / Neurexins and neuroligins / Sensory processing of sound by inner hair cells of the cochlea / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / positive regulation of calcium ion import / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / actin cytoskeleton / protein localization / cell-cell junction / presynaptic membrane / basolateral plasma membrane / 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 / non-specific serine/threonine protein kinase / calmodulin binding / cell adhesion / signaling receptor binding / protein serine kinase activity / focal adhesion / protein serine/threonine kinase activity / nucleolus / positive regulation of transcription by RNA polymerase II / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...CASK, SH3 domain / L27 domain, C-terminal / L27 domain / : / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Protein kinase domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-V62 / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 Å
AuthorsChaikuad, A. / Russ, N. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: J.Med.Chem. / Year: 2021
Title: Design and Development of a Chemical Probe for Pseudokinase Ca 2+ /calmodulin-Dependent Ser/Thr Kinase.
Authors: Russ, N. / Schroder, M. / Berger, B.T. / Mandel, S. / Aydogan, Y. / Mauer, S. / Pohl, C. / Drewry, D.H. / Chaikuad, A. / Muller, S. / Knapp, S.
History
DepositionApr 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peripheral plasma membrane protein CASK
B: Peripheral plasma membrane protein CASK
C: Peripheral plasma membrane protein CASK
D: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,38822
Polymers158,0224
Non-polymers3,36618
Water6,053336
1
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3786
Polymers39,5051
Non-polymers8735
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4407
Polymers39,5051
Non-polymers9356
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,2544
Polymers39,5051
Non-polymers7493
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3165
Polymers39,5051
Non-polymers8114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.460, 67.120, 126.800
Angle α, β, γ (deg.)89.940, 90.010, 90.290
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 6 - 303 / Label seq-ID: 22 - 319

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Peripheral plasma membrane protein CASK / hCASK / Calcium/calmodulin-dependent serine protein kinase / Protein lin-2 homolog


Mass: 39505.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CASK, LIN2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): CL21(DE3)-R3-pRARE2
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-V62 / 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclohexylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide


Mass: 624.368 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H32Br2N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.18 Å3/Da / Density % sol: 43.55 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 9% high molecular weight PEG Smears, 0.1 M magnesium acetate, 0.1 M KCl, 0.1 M MES, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→46.11 Å / Num. obs: 65093 / % possible obs: 92.2 % / Redundancy: 3.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.081 / Rrim(I) all: 0.15 / Net I/av σ(I): 6 / Net I/σ(I): 6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.17-2.2530.845260770.5250.6371.16487.1
8.4-46.113.20.0712050.9910.0430.08399

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C0I

3c0i


Resolution: 2.17→46.11 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.892 / SU B: 17.619 / SU ML: 0.22 / SU R Cruickshank DPI: 0.3404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.34 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2744 3205 4.9 %RANDOM
Rwork0.2206 ---
obs0.2232 61886 92.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 86.97 Å2 / Biso mean: 38.404 Å2 / Biso min: 20.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.08 Å2-0.23 Å2
2---0.51 Å2-0.22 Å2
3----0.31 Å2
Refinement stepCycle: final / Resolution: 2.17→46.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9512 0 200 336 10048
Biso mean--41.25 39.99 -
Num. residues----1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0139934
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179446
X-RAY DIFFRACTIONr_angle_refined_deg1.1911.63713380
X-RAY DIFFRACTIONr_angle_other_deg1.1281.59521842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22651188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24520.769520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.44151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3861580
X-RAY DIFFRACTIONr_chiral_restr0.0580.21208
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211252
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022188
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99240.02
12B99240.02
21A98010.04
22C98010.04
31A98180.04
32D98180.04
41B98120.04
42C98120.04
51B98220.04
52D98220.04
61C98960.02
62D98960.02
LS refinement shellResolution: 2.17→2.226 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 222 -
Rwork0.292 4392 -
all-4614 -
obs--88.2 %
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)
11.2305-0.2565-0.45611.4837-0.18631.76570.07920.08170.0589-0.0512-0.05390.0443-0.18540.0003-0.02530.0966-0.0221-0.02290.0160.01750.161432.604-11.456-99.863
21.2334-0.31210.48321.53630.24931.84060.08720.0579-0.0518-0.0488-0.047-0.03890.2043-0.0076-0.04030.0843-0.01790.03040.011-0.01910.160816.49538.815-36.465
31.53780.41070.77171.3810.09531.90910.0745-0.1435-0.10570.0991-0.02190.01580.1949-0.0383-0.05270.07280.00290.02440.01510.01740.160712.09821.26-80.347
41.66330.4531-0.78781.5199-0.04871.8580.0679-0.16760.11890.0994-0.0157-0.0292-0.18790.0496-0.05220.0558-0.0006-0.02280.0187-0.02150.1623-3.4676.111-16.974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 303
2X-RAY DIFFRACTION2B6 - 303
3X-RAY DIFFRACTION3C6 - 303
4X-RAY DIFFRACTION4D6 - 303

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