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- PDB-6t6f: Crystal structure of human calmodulin-dependent protein kinase 1D... -

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Basic information

Entry
Database: PDB / ID: 6t6f
TitleCrystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 8 (CS275)
ComponentsCalcium/calmodulin-dependent protein kinase type 1D
KeywordsTRANSFERASE / Inhibitor / Complex / Kinase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / positive regulation of neutrophil chemotaxis / regulation of neuron projection development / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development ...regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / calcium/calmodulin-dependent protein kinase activity / positive regulation of neutrophil chemotaxis / regulation of neuron projection development / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development / calmodulin binding / positive regulation of apoptotic process / inflammatory response / protein serine kinase activity / negative regulation of apoptotic process / signal transduction / ATP binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 / Alpha Beta
Similarity search - Domain/homology
Chem-MMW / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsSorrell, F. / Kraemer, A. / Butterworth, S. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202708 United Kingdom
CitationJournal: To Be Published
Title: CAMK1D bound to CS275
Authors: Sorrell, F. / Kraemer, A. / Butterworth, S. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Calcium/calmodulin-dependent protein kinase type 1D
B: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1594
Polymers73,3982
Non-polymers7612
Water3,711206
1
A: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0792
Polymers36,6991
Non-polymers3801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0792
Polymers36,6991
Non-polymers3801
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.950, 115.730, 53.960
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 12 through 33 or (resid 34...
21(chain B and ((resid 12 and (name CA or name...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRPALAALA(chain A and (resid 12 through 33 or (resid 34...AA12 - 335 - 26
12PHEPHEPHEPHE(chain A and (resid 12 through 33 or (resid 34...AA3427
13TRPTRPASPASP(chain A and (resid 12 through 33 or (resid 34...AA12 - 3285 - 322
14TRPTRPASPASP(chain A and (resid 12 through 33 or (resid 34...AA12 - 3285 - 322
15TRPTRPASPASP(chain A and (resid 12 through 33 or (resid 34...AA12 - 3285 - 322
16TRPTRPASPASP(chain A and (resid 12 through 33 or (resid 34...AA12 - 3285 - 322
17TRPTRPASPASP(chain A and (resid 12 through 33 or (resid 34...AA12 - 3285 - 322
21TRPTRPTRPTRP(chain B and ((resid 12 and (name CA or name...BB125
22TRPTRPASPASP(chain B and ((resid 12 and (name CA or name...BB12 - 3285 - 322
23TRPTRPASPASP(chain B and ((resid 12 and (name CA or name...BB12 - 3285 - 322

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Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1D / CaM kinase I delta / CaMKID / CaMKI-like protein kinase / CKLiK


Mass: 36698.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1D, CAMKID / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase
#2: Chemical ChemComp-MMW / 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3-(trifluoromethyl)phenyl]amino]pyrimidine-5-carboxamide


Mass: 380.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H19F3N6O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.34 Å3/Da / Density % sol: 47.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 28% PEG3350 -- 0.1M bis-tris pH 5.5 -- 0.2M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.97→48.91 Å / Num. obs: 49440 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 40.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Net I/σ(I): 14.7
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.646 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3587 / CC1/2: 0.526 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.13refinement
XDSdata reduction
xia2data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jc6

2jc6


Resolution: 1.97→48.905 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2376 2509 5.08 %
Rwork0.2099 46873 -
obs0.2113 49382 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.85 Å2 / Biso mean: 53.7188 Å2 / Biso min: 30.45 Å2
Refinement stepCycle: final / Resolution: 1.97→48.905 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4447 0 54 206 4707
Biso mean--44.66 53.11 -
Num. residues----575
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1650X-RAY DIFFRACTION8.473TORSIONAL
12B1650X-RAY DIFFRACTION8.473TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.97-2.00790.38951550.36892551100
2.0079-2.04890.33391640.3395251099
2.0489-2.09340.33421470.31262562100
2.0934-2.14210.30941430.2831255999
2.1421-2.19570.26991360.25592570100
2.1957-2.25510.23631220.25152585100
2.2551-2.32140.25561290.23672589100
2.3214-2.39640.24681200.22842588100
2.3964-2.4820.26341200.23712596100
2.482-2.58140.28341330.22852609100
2.5814-2.69880.25041330.23522607100
2.6988-2.84110.25471270.22522617100
2.8411-3.01910.23931290.22262598100
3.0191-3.25220.23391360.21592604100
3.2522-3.57940.22971790.20422601100
3.5794-4.09710.22361500.18192641100
4.0971-5.1610.21241430.16832664100
5.161-48.90.21481430.19742822100
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)
12.63630.27880.14262.27641.42572.77660.0764-0.5770.01030.15230.137-0.4490.06140.1293-0.20630.3738-0.0094-0.01440.43570.0160.4992-7.836527.2312-16.6684
23.6273-0.39470.66153.3950.3892.33670.0247-0.11820.1681-0.27860.0231-0.0233-0.1159-0.0539-0.05290.37480.00790.00660.3211-0.0120.3215-11.889516.6824-31.714
34.54091.3871-3.55588.0715-4.63244.42650.8038-1.5241-0.4251-0.0217-0.3563-0.3306-1.01040.93840.10360.5325-0.03620.04590.70390.02380.3685-13.11381.9464-17.4531
43.4551-0.71720.81533.2576-0.73822.16680.12160.0222-0.407-0.27050.02550.36610.1672-0.0505-0.15930.39120.0125-0.05770.2857-0.00110.4113-17.78381.9797-31.9046
50.78561.0893-1.42673.0068-3.69484.64520.31310.1261-0.02030.0655-0.00170.197-0.19680.1834-0.38270.4670.0509-0.06860.4964-0.02460.4977-24.876821.3326-44.289
63.3966-0.9836-1.29753.38870.08342.05510.05840.132-0.6894-0.2779-0.24950.43450.1848-0.06670.12120.473-0.0038-0.08830.50410.0160.7923-44.87111.9231-26.1579
75.37812.0886-2.83110.8676-1.0191.6062-0.2262-1.2932-0.19330.8982-0.29630.32890.98490.13450.18850.9456-0.1215-0.04171.12950.06670.9463-50.52979.534-9.4266
82.43910.16050.3752.12921.27310.7912-0.0051-0.3662-0.0684-0.0567-0.10430.4378-0.1062-0.37150.14590.37770.0352-0.04120.47740.04060.6131-46.287427.4862-15.6484
94.6736-0.20311.29452.0159-0.1113.3510.1381-0.3735-0.4456-0.0542-0.08570.18590.415-0.0931-0.04370.3824-0.01710.00310.44920.04060.5356-41.083726.0152-11.2612
103.462-0.281.12312.3524-1.0763.2320.0025-0.97360.41240.39180.00860.0843-0.1485-0.32590.00510.42670.00480.05060.6302-0.08930.5193-35.391535.5979-1.4084
111.60320.466-0.53737.623-3.45112.3389-0.0529-0.2660.1563-0.4153-0.1997-0.3520.03320.25880.14910.43020.0409-0.0360.4521-0.11020.6675-21.730747.4454-21.7646
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 12:108)A12 - 108
2X-RAY DIFFRACTION2(chain A and resid 109:185)A109 - 185
3X-RAY DIFFRACTION3(chain A and resid 186:199)A186 - 199
4X-RAY DIFFRACTION4(chain A and resid 200:286)A200 - 286
5X-RAY DIFFRACTION5(chain A and resid 287:328)A287 - 328
6X-RAY DIFFRACTION6(chain B and resid 12:56)B12 - 56
7X-RAY DIFFRACTION7(chain B and resid 57:73)B57 - 73
8X-RAY DIFFRACTION8(chain B and resid 74:142)B74 - 142
9X-RAY DIFFRACTION9(chain B and resid 143:198)B143 - 198
10X-RAY DIFFRACTION10(chain B and resid 199:294)B199 - 294
11X-RAY DIFFRACTION11(chain B and resid 295:328)B295 - 328

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