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- PDB-4aze: Human DYRK1A in complex with Leucettine L41 -

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Basic information

Entry
Database: PDB / ID: 4aze
TitleHuman DYRK1A in complex with Leucettine L41
Components(DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A) x 2
KeywordsTRANSFERASE
Function / homology
Function and homology information


regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization ...regulation of amyloid-beta formation / negative regulation of heterochromatin formation / regulation of neurofibrillary tangle assembly / histone H3T45 kinase activity / dual-specificity kinase / splicing factor binding / [RNA-polymerase]-subunit kinase / tau-protein kinase activity / regulation of alternative mRNA splicing, via spliceosome / negative regulation of microtubule polymerization / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / G0 and Early G1 / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / RNA polymerase II CTD heptapeptide repeat kinase activity / tubulin binding / peptidyl-tyrosine phosphorylation / positive regulation of RNA splicing / non-membrane spanning protein tyrosine kinase activity / circadian rhythm / tau protein binding / nervous system development / protein autophosphorylation / actin binding / protein tyrosine kinase activity / transcription coactivator activity / protein phosphorylation / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / centrosome / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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-3RA / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsElkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. ...Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Tahtouh, T. / Burgy, G. / Durieu, E. / Lozach, O. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Carreaux, F. / Bazureau, J.P. / Meijer, L. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Selectivity, Co-Crystal Structures and Neuroprotective Properties of Leucettines, a Family of Protein Kinase Inhibitors Derived from the Marine Sponge Alkaloid Leucettamine B.
Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / ...Authors: Tahtouh, T. / Elkins, J.M. / Filippakopoulos, P. / Soundararajan, M. / Burgy, G. / Durieu, E. / Cochet, C. / Schmid, R.S. / Lo, D.C. / Delhommel, F. / Oberholzer, A. / Laurence, P. / Carreaux, F. / Bazureau, J.P. / Knapp, S. / Meijer, L.
History
DepositionJun 25, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references / Derived calculations
Revision 1.2Nov 21, 2012Group: Database references
Revision 1.3Sep 8, 2021Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / reflns / 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_refine_tls_group.beg_auth_seq_id / _reflns.d_resolution_low / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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
Revision 1.4Dec 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
C: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
E: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
F: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
G: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,1439
Polymers135,2216
Non-polymers9223
Water00
1
A: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
E: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3813
Polymers45,0742
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
F: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3813
Polymers45,0742
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
G: DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A
hetero molecules


  • defined by author
  • 45.4 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)45,3813
Polymers45,0742
Non-polymers3071
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.649, 111.649, 301.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12E
22F
32G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A104 - 485
2111B104 - 485
3111C104 - 485
1121E890 - 910
2121F890 - 910
3121G890 - 910

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.48864, -0.87246, -0.00739), (0.80941, -0.45646, 0.36945), (-0.3257, 0.17455, 0.92922)-123.02924, -0.11578, -1.14655
2given(-0.9996, 0.02619, 0.01038), (0.02079, 0.93433, -0.35581), (-0.01902, -0.35545, -0.9345)-122.85606, 0.61943, -1.24844
3given(-0.99958, 0.021855, -0.019042), (0.027197, 0.934347, -0.355325), (0.010026, -0.355694, -0.934549)-122.811, 2.2944, 0.29767

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Components

#1: Protein DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A / DUAL SPECIFICITY YAK1-RELATED KINASE / HP86 / PROTEIN KINASE MINIBRAIN HOMOLOG / MNBH / HMNB


Mass: 44633.164 Da / Num. of mol.: 3 / Fragment: KINASE DOMAIN, RESIDUES 128-485
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13627, dual-specificity kinase, non-specific serine/threonine protein kinase
#2: Protein/peptide DUAL SPECIFICITY TYROSINE-PHOSPHORYLATION-REGULATED KINASE 1A / DUAL SPECIFICITY YAK1-RELATED KINASE / HP86 / PROTEIN KINASE MINIBRAIN HOMOLOG / MNBH / HMNB


Mass: 440.386 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: UNKNOWN PARTS OF THE N-TERMINUS / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: dual-specificity kinase, non-specific serine/threonine protein kinase
#3: Chemical ChemComp-3RA / 5-(1,3-benzodioxol-5-ylmethyl)-2-(phenylamino)-4H-imidazol-4-one


Mass: 307.303 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C17H13N3O3
Has protein modificationY
Sequence detailsUNKNOWN PARTS OF THE N-TERMINUS OF CHAINS A,B,C HAVE BEEN MODELLED AS CHAINS E,F,G

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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: 4.1 Å3/Da / Density % sol: 69.8 % / Description: NONE
Crystal growpH: 8.2
Details: 0.03 M MGCL2, 22% POLYACRYLIC ACID 5100, 0.1 M HEPES PH 8.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.984
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 3.15→100.57 Å / Num. obs: 37756 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 7.5
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.97 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX3

2vx3


Resolution: 3.15→100.57 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 49.158 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 1.813 / ESU R Free: 0.391 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24831 1883 5 %RANDOM
Rwork0.21755 ---
obs0.21904 35728 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 92.693 Å2
Baniso -1Baniso -2Baniso -3
1-2.68 Å21.34 Å20 Å2
2--2.68 Å20 Å2
3----4.03 Å2
Refinement stepCycle: LAST / Resolution: 3.15→100.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8544 0 69 0 8613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.028820
X-RAY DIFFRACTIONr_bond_other_d0.0020.026041
X-RAY DIFFRACTIONr_angle_refined_deg1.251.98111933
X-RAY DIFFRACTIONr_angle_other_deg0.8893.00114627
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0851053
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.5723.85413
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.327151521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5721555
X-RAY DIFFRACTIONr_chiral_restr0.0630.21266
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021837
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
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)
11A47003.59
12B47003.18
13C47003.71
22A3417.82
22B3413.38
22C347.82
LS refinement shellResolution: 3.15→3.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 126 -
Rwork0.34 2511 -
obs--99.77 %
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)
14.79090.7572-0.2493.29650.35488.27430.0151-0.45930.04090.29270.35990.13050.30860.1901-0.3750.2453-0.1071-0.03450.5254-0.10380.3037-42.036-23.08834.558
22.3812-0.0408-0.51133.12040.48685.52160.0272-0.3172-0.12360.11470.4233-0.36950.47021.1347-0.45040.07510.00920.00270.5417-0.29450.5292-26.407-28.35910.399
35.0513-0.7306-0.32184.2534-2.750110.45360.0579-0.0004-0.03890.3117-0.0533-0.2684-0.8236-0.6874-0.00460.37230.15950.05471.00360.15360.305-82.536-10.76240.526
44.7421-0.074-1.31972.3496-0.51285.15670.29790.68580.16030.12730.0229-0.3013-1.4845-1.2621-0.32070.48250.53140.13021.04090.35670.378-85.34-4.68912.134
54.78080.38750.56244.5111.49383.679-0.36131.9666-1.2944-0.85870.3943-0.77110.5645-1.4631-0.0330.7545-0.46620.38642.2224-0.72821.1875-81.371-34.204-24.394
64.03710.2728-1.35932.74550.40065.32-0.45791.5151-1.3571-0.06710.2865-0.23020.626-2.4910.17140.106-0.32140.17122.3188-0.19250.8801-97.083-30.004-0.427
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A133 - 241
2X-RAY DIFFRACTION2A242 - 481
3X-RAY DIFFRACTION3B135 - 241
4X-RAY DIFFRACTION4B242 - 481
5X-RAY DIFFRACTION5C133 - 241
6X-RAY DIFFRACTION6C242 - 481

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