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- PDB-4yfi: TNNI3K complexed with inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 4yfi
TitleTNNI3K complexed with inhibitor 1
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
N-methyl-3-(9H-purin-6-ylamino)benzenesulfonamide / Serine/threonine-protein kinase TNNI3K
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.7 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)150,2898
Polymers149,0724
Non-polymers1,2174
Water2,072115
1
A: Serine/threonine-protein kinase TNNI3K
B: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1454
Polymers74,5362
Non-polymers6092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Serine/threonine-protein kinase TNNI3K
D: Serine/threonine-protein kinase TNNI3K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,1454
Polymers74,5362
Non-polymers6092
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.069, 115.682, 92.015
Angle α, β, γ (deg.)90.000, 92.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D
13A
23B
33C
43D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A445 - 725
2115C445 - 725
1125B455 - 725
2125D455 - 725
1134A1
2134B1
3134C1
4134D1

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999998, 0.001737, -0.000383), (0.001734, 0.999977, 0.006498), (0.000394, 0.006498, -0.999979)-35.681759, 0.01113, -1.29575
3given(1), (1), (1)
4given(-0.999941, 0.001678, -0.010758), (0.001689, 0.999998, -0.001055), (0.010756, -0.001073, -0.999942)-35.912998, -0.09933, -1.18875
5given(1), (1), (1)
6given(0.056231, -0.489795, 0.870023), (-0.492526, -0.771601, -0.402554), (0.868479, -0.405873, -0.284624)-20.70323, 1.51873, 27.313181
7given(-0.999851, 0.010291, 0.013847), (0.010181, 0.999916, -0.008), (-0.013928, -0.007858, -0.999872)-35.647949, 0.25802, -1.74501
8given(-0.054774, -0.493639, -0.86794), (0.474124, -0.777858, 0.412484), (-0.878753, -0.388918, 0.276653)-23.920679, 19.407141, -3.1071

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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: 37267.977 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 503-831
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-4CW / N-methyl-3-(9H-purin-6-ylamino)benzenesulfonamide


Mass: 304.328 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H12N6O2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.86 Å3/Da / Density % sol: 57.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.3 M NaK tartrate, 0.1M HEPES pH7

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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: Jul 30, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 50917 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.075 / Χ2: 2.6 / Net I/av σ(I): 27.241 / Net I/σ(I): 18.7 / Num. measured all: 185934
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.6-2.693.60.46649482.59595.8
2.69-2.83.60.34950552.4596.2
2.8-2.933.60.24549962.43396.4
2.93-3.083.70.18250712.44396.6
3.08-3.283.70.1450432.47497.1
3.28-3.533.70.08851222.59297.6
3.53-3.883.70.05851122.797.7
3.88-4.453.60.04251312.6897.7
4.45-5.63.70.04251732.70598.5
5.6-5003.60.0452662.9198.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.7→37.82 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 22.659 / SU ML: 0.241 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.602 / ESU R Free: 0.324 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 2330 5.2 %RANDOM
Rwork0.2152 ---
obs0.2175 42439 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.99 Å2 / Biso mean: 48.295 Å2 / Biso min: 7.45 Å2
Baniso -1Baniso -2Baniso -3
1--1.15 Å20 Å21.32 Å2
2--1.29 Å2-0 Å2
3----0.23 Å2
Refinement stepCycle: final / Resolution: 2.7→37.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8287 0 84 115 8486
Biso mean--35.04 26.68 -
Num. residues----1060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0198610
X-RAY DIFFRACTIONr_bond_other_d0.0010.028195
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.97111687
X-RAY DIFFRACTIONr_angle_other_deg0.766318826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92151062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39323.804368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.684151430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.811542
X-RAY DIFFRACTIONr_chiral_restr0.0680.21302
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021995
X-RAY DIFFRACTIONr_mcbond_it1.9363.2634242
X-RAY DIFFRACTIONr_mcbond_other1.9363.2634241
X-RAY DIFFRACTIONr_mcangle_it3.4034.8765285
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1547MEDIUM POSITIONAL0.120.5
11A2546LOOSE POSITIONAL0.275
11A1547MEDIUM THERMAL2.512
11A2546LOOSE THERMAL2.8310
21B1485MEDIUM POSITIONAL0.130.5
21B2375LOOSE POSITIONAL0.295
21B1485MEDIUM THERMAL3.22
21B2375LOOSE THERMAL3.3210
31A33MEDIUM POSITIONAL0.180.5
32B33MEDIUM POSITIONAL0.180.5
33C33MEDIUM POSITIONAL0.280.5
34D33MEDIUM POSITIONAL0.260.5
31A33MEDIUM THERMAL24.32
32B33MEDIUM THERMAL29.642
33C33MEDIUM THERMAL24.252
34D33MEDIUM THERMAL18.962
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 168 -
Rwork0.326 3089 -
all-3257 -
obs--96.08 %
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)
11.820.4169-0.20140.247-0.25950.3592-0.1094-0.10910.1396-0.0710.0578-0.01170.101-0.02420.05150.12930.0308-0.03420.1627-0.06520.11365.32412.356.642
20.0289-0.1432-0.01131.8364-0.75180.82840.02060.01410.03160.05320.2376-0.01560.0123-0.1822-0.25810.14930.0115-0.05740.17190.0550.1484-23.229-12.48724.219
32.0837-0.5313-0.15020.32130.27320.3236-0.0759-0.03460.13490.03930.0485-0.00590.06610.0170.02730.1535-0.0038-0.01690.1210.05570.1123-41.16212.367-7.971
40.11740.27570.06131.13640.69770.78990.10130.04720.0190.17670.1083-0.07720.17980.0017-0.20960.34850.0126-0.09130.0582-0.00270.1033-12.357-12.405-25.527
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A441 - 726
2X-RAY DIFFRACTION2B451 - 729
3X-RAY DIFFRACTION3C441 - 726
4X-RAY DIFFRACTION4D451 - 729

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