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- PDB-7oak: Crystal structure of pseudokinase CASK in complex with compound 26 -

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Basic information

Entry
Database: PDB / ID: 7oak
TitleCrystal structure of pseudokinase CASK in complex with compound 26
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 / neurexin family protein binding / GMP kinase activity / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / 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 / neurexin family protein binding / GMP kinase activity / negative regulation of wound healing / Dopamine Neurotransmitter Release Cycle / 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 / Syndecan interactions / positive regulation of calcium ion import / regulation of synaptic vesicle exocytosis / basement membrane / negative regulation of cell-matrix adhesion / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / intracellular protein localization / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / 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 / cytoplasm / cytosol
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-V6B / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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

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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)161,70528
Polymers158,0224
Non-polymers3,68324
Water7,098394
1
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4267
Polymers39,5051
Non-polymers9216
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)40,4888
Polymers39,5051
Non-polymers9837
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)40,3646
Polymers39,5051
Non-polymers8595
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)40,4267
Polymers39,5051
Non-polymers9216
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.506, 67.147, 129.831
Angle α, β, γ (deg.)75.730, 89.960, 89.950
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-V6B / 2-[[2,5-bis(bromanyl)-4-methyl-phenyl]methylamino]-4-(cyclopentylamino)-N-[3-(2-oxidanylidene-1,3-oxazolidin-3-yl)propyl]pyrimidine-5-carboxamide


Mass: 610.341 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30Br2N6O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.17 Å3/Da / Density % sol: 43.21 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 12% high molecular weight PEG Smears, 0.1 M magnesium acetate, 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: 2.23→41.94 Å / Num. obs: 59635 / % possible obs: 92.3 % / Redundancy: 3 % / CC1/2: 0.983 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.104 / Rrim(I) all: 0.186 / Net I/av σ(I): 5.8 / Net I/σ(I): 5.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.23-2.292.80.784246060.6730.581.01392.5
9.72-41.943.20.0817570.9910.0510.09698.6

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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: 2.23→41.94 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.876 / SU B: 19.281 / SU ML: 0.235 / SU R Cruickshank DPI: 0.4097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.41 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2635 2933 4.9 %RANDOM
Rwork0.2225 ---
obs0.2246 56701 92.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.36 Å2 / Biso mean: 28.746 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.65 Å20.33 Å2
2---3.05 Å2-0.6 Å2
3---2.58 Å2
Refinement stepCycle: final / Resolution: 2.23→41.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9512 0 220 394 10126
Biso mean--33.82 29.92 -
Num. residues----1192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0139948
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179468
X-RAY DIFFRACTIONr_angle_refined_deg1.2541.63913388
X-RAY DIFFRACTIONr_angle_other_deg1.1331.59321888
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.70151188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.7520.769520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.677151728
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4481580
X-RAY DIFFRACTIONr_chiral_restr0.0630.21208
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)
11A99830.03
12B99830.03
21A99250.03
22C99250.03
31A99410.03
32D99410.03
41B99210.03
42C99210.03
51B99430.03
52D99430.03
61C99950.01
62D99950.01
LS refinement shellResolution: 2.23→2.288 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 228 -
Rwork0.313 4137 -
all-4365 -
obs--92.26 %
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)
10.88290.32710.2581.2535-0.21171.55180.0652-0.0845-0.04310.061-0.01920.00590.1413-0.0047-0.0460.08470.00950.01790.05090.04510.04495.642-5.429-16.687
20.8453-0.3027-0.24411.3126-0.23811.57290.05120.07750.0464-0.0738-0.0092-0.0002-0.1499-0.0067-0.04210.0898-0.0366-0.03110.04940.0440.041225.84-38.013-35.975
31.24620.3572-0.41231.61040.11941.71470.0652-0.11350.13220.06870.00150.0039-0.14440.0103-0.06670.0819-0.005-0.01480.05390.0190.044530.41-55.6546.282
41.251-0.2650.39071.39150.08851.65020.03990.1093-0.1218-0.06830.0041-0.00030.15180.0254-0.0440.0863-0.02380.00180.05540.01630.036210.194-22.95726.855
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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