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- PDB-2x7f: Crystal structure of the kinase domain of human Traf2- and Nck- i... -

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Basic information

Entry
Database: PDB / ID: 2x7f
TitleCrystal structure of the kinase domain of human Traf2- and Nck- interacting Kinase with Wee1Chk1 inhibitor
ComponentsTRAF2 AND NCK-INTERACTING PROTEIN KINASE
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHOPROTEIN / KINASE
Function / homology
Function and homology information


microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome ...microvillus assembly / regulation of dendrite morphogenesis / regulation of MAPK cascade / postsynaptic density, intracellular component / cytoskeleton organization / : / neuron projection morphogenesis / protein localization to plasma membrane / positive regulation of JNK cascade / recycling endosome / Wnt signaling pathway / MAPK cascade / presynapse / actin cytoskeleton organization / Oxidative Stress Induced Senescence / protein autophosphorylation / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / intracellular signal transduction / positive regulation of protein phosphorylation / apical plasma membrane / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / glutamatergic synapse / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...Domain found in NIK1-like kinases, mouse citron and yeast ROM1, ROM2 / CNH domain / Citron homology (CNH) domain / Citron homology (CNH) domain profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-824 / TRAF2 and NCK-interacting protein kinase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsVollmar, M. / Alfano, I. / Shrestha, B. / Bray, J. / Muniz, J.R.C. / Roos, A. / Filippakopoulos, P. / Burgess-Brown, N. / Ugochukwu, E. / Gileadi, O. ...Vollmar, M. / Alfano, I. / Shrestha, B. / Bray, J. / Muniz, J.R.C. / Roos, A. / Filippakopoulos, P. / Burgess-Brown, N. / Ugochukwu, E. / Gileadi, O. / Phillips, C. / Mahajan, P. / Pike, A.C.W. / Fedorov, O. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
CitationJournal: To be Published
Title: Crystal Structure of the Kinase Domain of Human Traf2- and Nck-Interacting Kinase with Wee1Chk1 Inhibitor
Authors: Vollmar, M. / Alfano, I. / Shrestha, B. / Bray, J. / Muniz, J.R.C. / Roos, A. / Filippakopoulos, P. / Burgess-Brown, N. / Ugochukwu, E. / Gileadi, O. / Phillips, C. / Mahajan, P. / Pike, A.C. ...Authors: Vollmar, M. / Alfano, I. / Shrestha, B. / Bray, J. / Muniz, J.R.C. / Roos, A. / Filippakopoulos, P. / Burgess-Brown, N. / Ugochukwu, E. / Gileadi, O. / Phillips, C. / Mahajan, P. / Pike, A.C.W. / Fedorov, O. / Chaikuad, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Knapp, S.
History
DepositionFeb 26, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
B: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
C: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
D: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
E: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,95915
Polymers186,2035
Non-polymers1,75710
Water30617
1
A: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5923
Polymers37,2411
Non-polymers3512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5923
Polymers37,2411
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5923
Polymers37,2411
Non-polymers3512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5923
Polymers37,2411
Non-polymers3512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TRAF2 AND NCK-INTERACTING PROTEIN KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5923
Polymers37,2411
Non-polymers3512
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.972, 79.074, 214.159
Angle α, β, γ (deg.)90.00, 91.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
TRAF2 AND NCK-INTERACTING PROTEIN KINASE


Mass: 37240.586 Da / Num. of mol.: 5 / Fragment: KINASE DOMAIN, RESIDUES 1-325
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): MACH1
References: UniProt: Q9UKE5, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-824 / 9-HYDROXY-4-PHENYLPYRROLO[3,4-C]CARBAZOLE-1,3(2H,6H)-DIONE / 9-HYDROXY-4-PHENYL-6H-PYRROLO[3,4-C]CARBAZOLE-1,3-DIONE


Mass: 328.321 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H12N2O3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE STARTS WITH A SER AS A RESULT OF VECTOR CONSTRUCTION

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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: 2.49 Å3/Da / Density % sol: 50.64 % / Description: NONE
Crystal growDetails: 150 MM NA-MALONATE (PH 7.0), 25% (W/V) PEG 3350, 5% (V/V) ETHYLENE GLYCOL, 100 MM BIS-TRIS-PROPANE (PH 9.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 5, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999 Å / Relative weight: 1
ReflectionResolution: 2.8→45.85 Å / Num. obs: 44037 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 83.39 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 14
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER-TNT2.8.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3COM

3com


Resolution: 2.8→44.32 Å / Cor.coef. Fo:Fc: 0.9167 / Cor.coef. Fo:Fc free: 0.9084 / Cross valid method: THROUGHOUT / σ(F): 0
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DRG NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9237. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=125. NUMBER ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=DRG NA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9237. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=125. NUMBER TREATED BY BAD NON-BONDED CONTACTS=5.
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2016 4.6 %RANDOM
Rwork0.2093 ---
obs0.2102 43783 --
Displacement parametersBiso mean: 94.35 Å2
Baniso -1Baniso -2Baniso -3
1--15.2383 Å20 Å2-1.8457 Å2
2---0.1844 Å20 Å2
3---15.4228 Å2
Refine analyzeLuzzati coordinate error obs: 0.449 Å
Refinement stepCycle: LAST / Resolution: 2.8→44.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9213 0 130 17 9360
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099566HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1113102HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2790SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes199HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1525HARMONIC5
X-RAY DIFFRACTIONt_it9566HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.4
X-RAY DIFFRACTIONt_other_torsion19.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1361SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact10094SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2143 144 4.55 %
Rwork0.229 3024 -
all0.2283 3168 -
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)
13.0891-1.4612-1.44331.29390.03234.6042-0.02880.063-0.043-0.0216-0.0304-0.12230.00090.08260.05920.01570.23720.1425-0.1340.1468-0.01632.8589-3.517564.3712
22.18870.26170.6290.5514-0.0773.27090.00050.0144-0.02-0.04750.03430.05340.026-0.1241-0.0348-0.01410.13790.04760.04860.0382-0.077618.5275-0.27551.2636
30.94340.32631.72080.1581-1.07812.9495-0.01820.0965-0.0205-0.0805-0.00060.0791-0.017-0.11420.0188-0.00150.1936-0.07070.15220.1561-0.180314.44414.358142.6527
40.60151.4566-0.81215.587-0.97033.99480.06160.0254-0.10390.024-0.0987-0.04130.13430.18520.0371-0.23060.024-0.0131-0.15340.02050.279411.1115-20.6502107.2087
52.95070.1941-0.89224.3848-1.14632.6590.05260.0740.0741-0.03230.03730.1099-0.02730.0107-0.0899-0.23440.01050.0046-0.16650.03310.250911.1961-4.966693.4781
62.5519-1.013-2.68582.6422-0.93043.59610.02610.24010.2853-0.2363-0.03110.141-0.1371-0.0650.005-0.23460.0626-0.0092-0.21380.02460.263710.61261.617587.0708
72.1095-0.2887-0.73721.48960.07681.9784-0.00660.0925-0.0399-0.02150.0971-0.08230.16180.0752-0.0905-0.06760.23690.13550.0730.1452-0.05157.1154-44.980664.6922
82.61570.1225-0.77722.658-3.14111.68840.03720.15480.1062-0.02250.07110.0106-0.0788-0.0227-0.1083-0.05280.19560.1906-0.2010.21210.2172-7.2026-36.425376.2941
90.9546-1.18980.06795.8849-3.33921.42030.05290.0820.13550.17320.09810.1528-0.1175-0.2004-0.1511-0.02850.160.2837-0.26480.13710.2133-13.6082-39.190684.9616
100.0041.3123-0.11650.0008-0.68183.41490.00620.01020.0544-0.0390.0099-0.0705-0.03140.0069-0.01610.1637-0.0312-0.08130.11330.0829-0.2395-1.2447-18.651721.5849
110.5015-0.85710.97630.7349-0.79954.07940.00490.01260.0065-0.003-0.01170.0753-0.02250.02580.00680.13280.1271-0.11230.0660.0785-0.2035-9.4764-27.629834.638
120.48370.92490.57740.3342-1.8654.1628-0.0038-0.0677-0.03210.0179-0.00080.07990.0824-0.05570.00460.10190.1094-0.0580.09960.0814-0.2247-10.5686-35.230443.4187
13-0.08312.70051.48550.0039-0.66745.5508-0.0069-0.02790.0841-0.0201-0.0154-0.07070.0225-0.0080.02230.1541-0.0793-0.14080.10190.0922-0.264425.44121.886621.7479
140.05840.65770.86520.35440.62032.6019-0.00370.0055-0.0455-0.0248-0.0096-0.02730.0142-0.02370.01330.1506-0.1377-0.05810.10020.0138-0.210417.87269.99258.9028
15-0.1383-0.28532.07990.47291.7792.3297-0.00260.019-0.0637-0.05690.0015-0.0220.0156-0.03060.00110.1595-0.1597-0.05310.07090.0698-0.215712.51976.6903-0.5788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(A:15 - A:109 )
2X-RAY DIFFRACTION2(A:110 - A:198 )
3X-RAY DIFFRACTION3(A:197 - A:311 )
4X-RAY DIFFRACTION4(B:14 - B:109 )
5X-RAY DIFFRACTION5(B:110 - B:207 )
6X-RAY DIFFRACTION6(B:208 - B:311 )
7X-RAY DIFFRACTION7(C:14 - C:109 )
8X-RAY DIFFRACTION8(C:110 - C:191 )
9X-RAY DIFFRACTION9(C:192 - C:311 )
10X-RAY DIFFRACTION10(D:17 - D:109 )
11X-RAY DIFFRACTION11(D:110 - D:196 )
12X-RAY DIFFRACTION12(D:197 - D:306 )
13X-RAY DIFFRACTION13(E:14 - E:109 )
14X-RAY DIFFRACTION14(E:110 - E:196 )
15X-RAY DIFFRACTION15(E:197 - E:309 )

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