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

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Basic information

Entry
Database: PDB / ID: 7oaj
TitleCrystal structure of pseudokinase CASK in complex with compound 7
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 / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...negative regulation of cellular response to growth factor stimulus / guanylate kinase activity / Dopamine Neurotransmitter Release Cycle / neurexin family protein binding / regulation of neurotransmitter secretion / negative regulation of wound healing / nuclear lamina / calcium ion import / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Sensory processing of sound by outer hair cells of the cochlea / Sensory processing of sound by inner hair cells of the cochlea / Nephrin family interactions / ciliary membrane / regulation of synaptic vesicle exocytosis / Syndecan interactions / negative regulation of cell-matrix adhesion / positive regulation of calcium ion import / basement membrane / negative regulation of keratinocyte proliferation / establishment of localization in cell / Schaffer collateral - CA1 synapse / nuclear matrix / cell-cell junction / actin cytoskeleton / presynaptic membrane / basolateral plasma membrane / vesicle / calmodulin binding / non-specific serine/threonine protein kinase / cell adhesion / phosphorylation / 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. / Guanylate kinase-like domain profile. ...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-V6E / Peripheral plasma membrane protein CASK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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)161,40930
Polymers158,0224
Non-polymers3,38726
Water9,890549
1
A: Peripheral plasma membrane protein CASK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3838
Polymers39,5051
Non-polymers8787
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)40,50710
Polymers39,5051
Non-polymers1,0029
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)40,3217
Polymers39,5051
Non-polymers8166
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)40,1975
Polymers39,5051
Non-polymers6924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.355, 66.844, 130.203
Angle α, β, γ (deg.)76.200, 89.990, 90.000
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: 0 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA6 - 30122 - 317
21BB6 - 30122 - 317
12AA6 - 30122 - 317
22CC6 - 30122 - 317
13AA6 - 30122 - 317
23DD6 - 30122 - 317
14BB6 - 30222 - 318
24CC6 - 30222 - 318
15BB6 - 30222 - 318
25DD6 - 30222 - 318
16CC6 - 30222 - 318
26DD6 - 30222 - 318

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 BL21(DE3) (bacteria) / Variant (production host): -R3-pRARE2
References: UniProt: O14936, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-V6E / 4-(cyclopentylamino)-2-[(3,4-dichlorophenyl)methylamino]-N-[3-(2-oxidanylidenepyrrolidin-1-yl)propyl]pyrimidine-5-carboxamide


Mass: 505.440 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H30Cl2N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 549 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9% medium molecular weight PED Smears, 0.1 M magnesium acetate, 10% ethylene glycol, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99986 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99986 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.542
11h,-k,-l20.458
ReflectionResolution: 1.93→42.15 Å / Num. obs: 93376 / % possible obs: 91.6 % / Redundancy: 3.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.043 / Rrim(I) all: 0.085 / Net I/av σ(I): 9.9 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.9 %

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.93-20.492290950.8310.3570.70690.6
7.47-42.150.0517490.9950.0290.05899.3

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0222refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C0I

3c0i


Resolution: 1.93→42.15 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.922 / SU ML: 0.081 / SU R Cruickshank DPI: 0.0388 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2238 4466 4.8 %RANDOM
Rwork0.1946 ---
obs0.196 88899 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 79.6 Å2 / Biso mean: 34.554 Å2 / Biso min: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1-8.97 Å20.47 Å20.33 Å2
2---18.56 Å20.72 Å2
3---9.59 Å2
Refinement stepCycle: final / Resolution: 1.93→42.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9497 0 224 549 10270
Biso mean--35.44 36.07 -
Num. residues----1189
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0149990
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179205
X-RAY DIFFRACTIONr_angle_refined_deg1.2911.6513449
X-RAY DIFFRACTIONr_angle_other_deg0.9021.66321561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79651201
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.84420.798526
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.299151746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.6311581
X-RAY DIFFRACTIONr_chiral_restr0.080.21215
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211402
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021878
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99970.05
12B99970.05
21A100390.05
22C100390.05
31A100100.05
32D100100.05
41B101060.05
42C101060.05
51B100610.05
52D100610.05
61C100450.06
62D100450.06
LS refinement shellResolution: 1.93→1.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.282 296 -
Rwork0.214 6590 -
all-6886 -
obs--90.26 %
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)
10.1220.14210.14960.38210.09080.4504-0.001-0.02320.00650.0249-0.02230.06030.0029-0.00660.02340.06860.01980.03180.01160.00980.02724.52838.35536.355
20.1359-0.1183-0.11910.42940.06940.383-0.00190.02580.012-0.0259-0.01650.052-0.0059-0.00560.01840.0640.0132-0.00050.00970.00720.01823.8695.98617.123
30.2104-0.09760.15130.5372-0.06190.3697-0.020.0522-0.0232-0.01370.0235-0.0620.00370.007-0.00350.07250.00650.03580.0251-0.00770.026630.356.209-46.148
40.28590.1023-0.19940.5971-0.12290.4338-0.0093-0.05220.02310.0224-0.0088-0.0643-0.010.00670.01810.07110.0262-0.0010.02-0.00680.01419.59723.837-26.765
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 303
2X-RAY DIFFRACTION2B6 - 302
3X-RAY DIFFRACTION3C6 - 302
4X-RAY DIFFRACTION4D6 - 302

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