[English] 日本語
Yorodumi
- PDB-5aik: Human DYRK1A in complex with LDN-211898 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5aik
TitleHuman DYRK1A in complex with LDN-211898
ComponentsDYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
KeywordsTRANSFERASE / DYRK1A / KINASE
Function / homology
Function and homology information


histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome ...histone H3T45 kinase activity / positive regulation of protein deacetylation / peptidyl-serine autophosphorylation / negative regulation of DNA methylation-dependent heterochromatin formation / dual-specificity kinase / [RNA-polymerase]-subunit kinase / negative regulation of microtubule polymerization / tau-protein kinase activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of mRNA splicing, via spliceosome / amyloid-beta formation / G0 and Early G1 / peptidyl-tyrosine autophosphorylation / cytoskeletal protein binding / protein serine/threonine/tyrosine kinase activity / tubulin binding / RNA polymerase II CTD heptapeptide repeat kinase activity / positive regulation of RNA splicing / peptidyl-threonine phosphorylation / non-membrane spanning protein tyrosine kinase activity / tau protein binding / circadian rhythm / peptidyl-tyrosine phosphorylation / : / nervous system development / actin binding / peptidyl-serine phosphorylation / protein tyrosine kinase activity / protein autophosphorylation / transcription coactivator activity / cytoskeleton / protein kinase activity / nuclear speck / ribonucleoprotein complex / axon / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / dendrite / positive regulation of DNA-templated transcription / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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 ...Dual specificity tyrosine-phosphorylation-regulated kinase 1A/1B, catalytic domain / 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-AWR / PHOSPHATE ION / Dual specificity tyrosine-phosphorylation-regulated kinase 1A
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsElkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Cuny, G. / Higgins, J. / Edwards, A. / Bountra, C. / Knapp, S.
CitationJournal: To be published
Title: Dyrk1A with Ldn-211898
Authors: Elkins, J.M. / Soundararajan, M. / Muniz, J.R.C. / Cuny, G. / Higgins, J. / Edwards, A. / Bountra, C. / Knapp, S.
History
DepositionFeb 15, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Jul 7, 2021Group: Derived calculations / Other / Refinement description
Category: pdbx_database_status / pdbx_refine_tls_group ...pdbx_database_status / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_conn / struct_site
Item: _pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.beg_auth_seq_id ..._pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Jan 10, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
B: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
C: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
D: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,51218
Polymers178,2134
Non-polymers2,29914
Water1,15364
1
A: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0804
Polymers44,5531
Non-polymers5273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1755
Polymers44,5531
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0804
Polymers44,5531
Non-polymers5273
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,1755
Polymers44,5531
Non-polymers6224
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.955, 90.891, 232.468
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: 0

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA134 - 48131 - 378
21BB134 - 48131 - 378
12AA134 - 48131 - 378
22CC134 - 48131 - 378
13AA134 - 48031 - 377
23DD134 - 48031 - 377
14BB134 - 48131 - 378
24CC134 - 48131 - 378
15BB134 - 48031 - 377
25DD134 - 48031 - 377
16CC134 - 48031 - 377
26DD134 - 48031 - 377

NCS ensembles :
ID
1
2
3
4
5
6

NCS oper:
IDCodeMatrixVector
1given(0.45407, -0.62824, 0.63177), (0.67343, -0.22227, -0.70504), (0.58336, 0.74559, 0.32215)-5.22992, 30.03312, 31.1637
2given(-0.70366, 0.25188, 0.6644), (0.41962, -0.60727, 0.67464), (0.5734, 0.75351, 0.32162)-9.69246, 58.36529, -26.22789
3given(0.22031, -0.97518, -0.02218), (-0.97488, -0.22089, 0.02843), (-0.03263, 0.01536, -0.99935)61.96759, 75.63342, 57.6227

-
Components

#1: Protein
DYRK1A DUAL-SPECIFICITY TYROSINE-PHOSPHORYLATION REGULATED KINASE 1A / DUAL SPECIFICITY YAK1-RELATED KINASE / HP86 / PROTEIN KINASE MINIBRAIN HOMOLOG / MNBH / HMNB


Mass: 44553.188 Da / Num. of mol.: 4 / Fragment: KINASE DOMAIN, UNP 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, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-AWR / 4-(7-METHOXY-1-(TRIFLUOROMETHYL)-9H-PYRIDO[3,4-B]INDOL-9-yl)butan-1-amine


Mass: 337.340 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18F3N3O
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2M NA/KPO4, 20% PEG 3350, 10% ETHYLENE GLYCOL, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9245
DetectorType: DECTRIS PIXEL / Detector: PIXEL / Date: Jul 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9245 Å / Relative weight: 1
ReflectionResolution: 2.7→45.45 Å / Num. obs: 52473 / % possible obs: 98.6 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.3 / % possible all: 95.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VX3

2vx3


Resolution: 2.7→116.23 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.883 / SU B: 31.149 / SU ML: 0.288 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25222 2665 5.1 %RANDOM
Rwork0.22681 ---
obs0.22808 49699 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.729 Å2
Baniso -1Baniso -2Baniso -3
1-0.67 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→116.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11111 0 146 64 11321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01911519
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210913
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.96615592
X-RAY DIFFRACTIONr_angle_other_deg1.2272.99125054
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98851366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83523.966537
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.699152001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3651566
X-RAY DIFFRACTIONr_chiral_restr0.210.21658
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112880
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022714
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_it0.6131.8595488
X-RAY DIFFRACTIONr_mcbond_other0.6131.8595487
X-RAY DIFFRACTIONr_mcangle_it1.1192.7846846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.5611.9546031
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: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A429820.04
12B429820.04
21A432480.04
22C432480.04
31A431280.05
32D431280.05
41B431420.04
42C431420.04
51B428380.04
52D428380.04
61C430580.05
62D430580.05
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 195 -
Rwork0.327 3599 -
obs--97.71 %
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)
10.90880.1009-0.00972.461-0.3393.72570.0513-0.2774-0.11780.1267-0.102-0.123-0.00210.22090.05060.1154-0.00770.05970.13280.07510.090319.33629.56238.926
21.23990.5028-0.27712.7265-0.10942.63930.01540.0775-0.1008-0.2685-0.12650.03710.1406-0.11290.11110.11940.03370.04070.02530.00330.061113.94724.7949.46
33.360.01160.37813.6782-0.77984.4475-0.0910.1656-0.1995-0.2375-0.1512-0.38990.26060.41040.24230.1530.090.16160.08350.10090.2419.6079.19977.383
41.392-0.096-0.35091.4086-0.46363.071-0.00010.12660.04380.008-0.00160.0668-0.1908-0.16450.00180.140.00680.07060.06860.04120.0777-8.26927.00360.731
51.622-0.1983-0.07255.14460.49932.91760.09860.0457-0.04810.00760.0571-0.1064-0.09840.1484-0.15570.0678-0.00360.02490.0145-0.02760.07519.94474.91719.882
62.34010.2763-0.16941.78760.45041.86-0.02190.4875-0.3162-0.2894-0.30120.4541-0.0413-0.3480.32310.22070.0638-0.10980.2216-0.23310.3031-6.83155.5863.504
72.55731.30160.60132.2411.27722.4187-0.0272-0.08110.064-0.33160.089-0.1415-0.40840.0651-0.06180.24-0.06160.12940.1071-0.00190.141436.42450.96418.647
81.7659-0.1520.47512.3112-0.32133.0237-0.0261-0.62080.02010.21030.2245-0.3454-0.24240.1078-0.19840.1804-0.0620.05860.4659-0.16340.213641.05157.06247.976
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A134 - 241
2X-RAY DIFFRACTION2A242 - 481
3X-RAY DIFFRACTION3B134 - 241
4X-RAY DIFFRACTION4B242 - 481
5X-RAY DIFFRACTION5C134 - 241
6X-RAY DIFFRACTION6C242 - 481
7X-RAY DIFFRACTION7D134 - 241
8X-RAY DIFFRACTION8D242 - 480

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more