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- PDB-4yff: TNNI3K complexed with inhibitor 2 -

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Basic information

Entry
Database: PDB / ID: 4yff
TitleTNNI3K complexed with inhibitor 2
ComponentsSerine/threonine-protein kinase TNNI3K
KeywordsTransferase/Transferase Inhibitor / kinase / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


bundle of His cell to Purkinje myocyte communication / peptidyl-serine autophosphorylation / regulation of cardiac conduction / regulation of cardiac muscle contraction / regulation of heart rate / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity ...bundle of His cell to Purkinje myocyte communication / peptidyl-serine autophosphorylation / regulation of cardiac conduction / regulation of cardiac muscle contraction / regulation of heart rate / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site ...Ankyrin repeats (many copies) / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Chem-4CV / Serine/threonine-protein kinase TNNI3K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.07 Å
AuthorsShewchuk, L.M. / Wang, L. / Lawhorn, B.G.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Identification of Purines and 7-Deazapurines as Potent and Selective Type I Inhibitors of Troponin I-Interacting Kinase (TNNI3K).
Authors: Lawhorn, B.G. / Philp, J. / Zhao, Y. / Louer, C. / Hammond, M. / Cheung, M. / Fries, H. / Graves, A.P. / Shewchuk, L. / Wang, L. / Cottom, J.E. / Qi, H. / Zhao, H. / Totoritis, R. / Zhang, G. ...Authors: Lawhorn, B.G. / Philp, J. / Zhao, Y. / Louer, C. / Hammond, M. / Cheung, M. / Fries, H. / Graves, A.P. / Shewchuk, L. / Wang, L. / Cottom, J.E. / Qi, H. / Zhao, H. / Totoritis, R. / Zhang, G. / Schwartz, B. / Li, H. / Sweitzer, S. / Holt, D.A. / Gatto, G.J. / Kallander, L.S.
History
DepositionFeb 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 7, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase TNNI3K
B: Serine/threonine-protein kinase TNNI3K
C: Serine/threonine-protein kinase TNNI3K
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,4238
Polymers139,5534
Non-polymers1,8694
Water34219
1
A: Serine/threonine-protein kinase TNNI3K
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7114
Polymers69,7772
Non-polymers9352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase TNNI3K
C: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7114
Polymers69,7772
Non-polymers9352
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.447, 106.071, 93.239
Angle α, β, γ (deg.)90.00, 93.78, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F
33G
43H

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A445 - 725
2111B445 - 725
1121C455 - 725
2121D455 - 725
1131E1
2131F1
3131G1
4131H1

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.999986, -0.005281, 0.000883), (0.005325, 0.99805, -0.06219), (-0.000553, 0.062194, 0.998064)38.783119, -52.748131, -5.72273
3given(0.194156, -0.553357, -0.81), (-0.506279, -0.76377, 0.40042), (-0.840229, 0.332342, -0.428444)78.121773, -5.72037, 23.87322
4given(0.174494, -0.546632, -0.818991), (-0.564708, -0.736927, 0.371542), (-0.806633, 0.397659, -0.437277)39.1992, -20.191351, 72.149117

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Components

#1: Protein
Serine/threonine-protein kinase TNNI3K / Cardiac ankyrin repeat kinase / Cardiac troponin I-interacting kinase / TNNI3-interacting kinase


Mass: 34888.363 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 521-831
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TNNI3K, CARK / Plasmid: pFASTBAC / Production host: unidentified baculovirus
References: UniProt: Q59H18, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-4CV / 3-[(5-bromo-7H-pyrrolo[2,3-d]pyrimidin-4-yl)amino]-N-methyl-4-(morpholin-4-yl)benzenesulfonamide


Mass: 467.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H19BrN6O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 3.02 Å3/Da / Density % sol: 59.27 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 8% PEG3350, 0.1M ammonium sulfate, and 0.1M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.06→50 Å / Num. obs: 30089 / % possible obs: 99.1 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.099 / Χ2: 2.233 / Net I/av σ(I): 20.486 / Net I/σ(I): 11 / Num. measured all: 103684
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.06-3.23.50.77914671.7599.9
3.2-3.263.50.57415481.549100
3.26-3.333.60.54814751.72899.9
3.33-3.393.50.39515421.79100
3.39-3.473.60.3614911.80399.8
3.47-3.553.60.27315111.88199.8
3.55-3.643.60.21414981.97799.7
3.64-3.733.50.19115262.05799.8
3.73-3.843.60.16614762.18599.9
3.84-3.973.50.14115322.13499.7
3.97-4.113.50.12315002.33499.6
4.11-4.273.40.09815122.43599.5
4.27-4.473.40.08915012.69298.5
4.47-4.73.30.07914892.72199.1
4.7-53.30.07515012.54598.9
5-5.383.40.07315112.57499.2
5.38-5.933.40.0715252.46999.3
5.93-6.783.40.06515172.51599.3
6.78-8.543.20.04715102.74198.7
8.54-502.80.03914573.36892.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.07→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / SU B: 39.507 / SU ML: 0.327 / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 1512 5 %RANDOM
Rwork0.209 ---
obs0.211 28481 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 83.21 Å2
Baniso -1Baniso -2Baniso -3
1--5.3 Å20 Å20.07 Å2
2--8.17 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 3.07→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8089 0 112 19 8220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0198412
X-RAY DIFFRACTIONr_bond_other_d0.0070.027896
X-RAY DIFFRACTIONr_angle_refined_deg1.2311.9711428
X-RAY DIFFRACTIONr_angle_other_deg0.888318127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75851033
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0123.768353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.353151352
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0741539
X-RAY DIFFRACTIONr_chiral_restr0.0760.21270
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219540
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021923
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.666.7134162
X-RAY DIFFRACTIONr_mcbond_other3.6586.7124161
X-RAY DIFFRACTIONr_mcangle_it6.00410.0485182
X-RAY DIFFRACTIONr_mcangle_other6.00410.0495183
X-RAY DIFFRACTIONr_scbond_it3.5926.944250
X-RAY DIFFRACTIONr_scbond_other3.4996.9414127
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.71510.2856066
X-RAY DIFFRACTIONr_long_range_B_refined8.88953.2569562
X-RAY DIFFRACTIONr_long_range_B_other8.69752.7449336
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A39833.95
21C38314.86
33A288.31
33B284.1
33C2812.52
33D284.04
LS refinement shellResolution: 3.07→3.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 62 -
Rwork0.341 1253 -
obs--57.4 %
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)
12.620.32320.49860.14270.23140.4038-0.1022-0.0961-0.2564-0.06340.0178-0.001-0.1244-0.01510.08450.1552-0.01410.00760.0209-0.01050.216639.003-37.6523.234
22.17380.16780.64050.06450.09490.2566-0.0954-0.2891-0.261-0.06050.0719-0.008-0.103-0.02830.02350.1316-0.00540.02080.14050.09510.21460.1815.6058.116
30.10290.12370.22440.6360.56681.62670.04180.0865-0.07040.14340.11170.0674-0.34760.2016-0.15340.2822-0.00750.0620.1213-0.05420.108626.02938.89727.749
40.19060.07150.03530.87210.17290.58570.11120.0835-0.06440.2385-0.02510.0335-0.03330.0609-0.08610.2276-0.0050.02570.0657-0.01760.153165.661-14.50423.857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A445 - 726
2X-RAY DIFFRACTION2B445 - 726
3X-RAY DIFFRACTION3C452 - 725
4X-RAY DIFFRACTION4D452 - 726

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