[English] 日本語
Yorodumi
- PDB-6ft7: Crystal structure of CLK3 in complex with compound 8a -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ft7
TitleCrystal structure of CLK3 in complex with compound 8a
ComponentsDual specificity protein kinase CLK3
KeywordsTRANSFERASE / kinase / inhibitor / splicing kinase / CLK / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity ...dual-specificity kinase / intermediate filament cytoskeleton / regulation of RNA splicing / protein serine/threonine/tyrosine kinase activity / acrosomal vesicle / protein tyrosine kinase activity / protein phosphorylation / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / membrane
Similarity search - Function
: / 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. ...: / 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 / Alpha Beta
Similarity search - Domain/homology
3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one / IODIDE ION / Dual specificity protein kinase CLK3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsChaikuad, A. / Walter, A. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Edwards, A.M. / Kunick, C. / Knapp, S. / Structural Genomics Consortium (SGC)
CitationJournal: PLoS ONE / Year: 2018
Title: Molecular structures of cdc2-like kinases in complex with a new inhibitor chemotype.
Authors: Walter, A. / Chaikuad, A. / Helmer, R. / Loaec, N. / Preu, L. / Ott, I. / Knapp, S. / Meijer, L. / Kunick, C.
History
DepositionFeb 20, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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: Dual specificity protein kinase CLK3
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,65130
Polymers84,6372
Non-polymers3,01428
Water8,737485
1
A: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,63912
Polymers42,3181
Non-polymers1,32111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dual specificity protein kinase CLK3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,01218
Polymers42,3181
Non-polymers1,69317
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.760, 116.830, 69.910
Angle α, β, γ (deg.)90.00, 92.75, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERGLUGLUAA129 - 2375 - 113
21SERSERGLUGLUBB129 - 2375 - 113
12LEULEUARGARGAA238 - 480114 - 356
22LEULEUARGARGBB238 - 480114 - 356

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.999991, 0.003927, 0.001666), (-0.003969, -0.999653, -0.026031), (0.001563, -0.026037, 0.99966)88.80568, 148.12427, 1.89425
3given(1), (1), (1)
4given(-0.999918, 0.008771, 0.00928), (-0.008914, -0.999839, -0.015566), (0.009142, -0.015647, 0.999836)87.96809, 147.70662, 0.53903

-
Components

#1: Protein Dual specificity protein kinase CLK3 / CDC-like kinase 3


Mass: 42318.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLK3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): R3-pRARE2 / References: UniProt: P49761, dual-specificity kinase
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-E6Q / 3-phenyl-1~{H}-pyrrolo[3,4-g]indol-8-one


Mass: 246.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10N2O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2.98 Å3/Da / Density % sol: 58.68 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 21% PEG3350, 0.2 M sodium iodide, 0.1 M bis-tris-propane pH 7.0, 10% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→59.95 Å / Num. obs: 62659 / % possible obs: 96.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 29 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 8
Reflection shellResolution: 2.02→2.13 Å / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9103 / % possible all: 96

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EU9

2eu9


Resolution: 2.02→58.41 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.305 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23523 3185 5.1 %RANDOM
Rwork0.1917 ---
obs0.19395 59444 96.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 42.83 Å2
Baniso -1Baniso -2Baniso -3
1--2.86 Å20 Å2-0.21 Å2
2--1.57 Å20 Å2
3---1.27 Å2
Refinement stepCycle: 1 / Resolution: 2.02→58.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5800 0 100 485 6385
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196144
X-RAY DIFFRACTIONr_bond_other_d0.0010.024272
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.948301
X-RAY DIFFRACTIONr_angle_other_deg0.96310335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.65523.491318
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.748151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7391544
X-RAY DIFFRACTIONr_chiral_restr0.0980.2870
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021349
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_free47.09257
X-RAY DIFFRACTIONr_sphericity_bonded83.63957
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1441medium positional0.330.5
22B3387medium positional0.280.5
11A1441medium thermal2.142
22B3387medium thermal2.432
LS refinement shellResolution: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 206 -
Rwork0.303 4311 -
obs--95.5 %
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)
12.34090.28490.5591.6057-0.58381.0072-0.14890.24860.43280.22590.0087-0.1737-0.02680.03710.14020.08430.0086-0.05870.10.04290.293158.35574.181555.9968
21.1253-0.1998-0.29190.45840.35930.444-0.03250.2265-0.17190.1418-0.07110.00430.0299-0.08030.10350.1143-0.012-0.00310.1716-0.02170.129457.682147.348848.8938
39.6622-11.143111.292324.79944.956840.4378-0.9498-1.87661.15660.91010.269-1.3358-0.4365-3.99710.68080.7371-0.60950.41251.4658-0.45450.617257.068144.162170.7614
41.5852-1.1184-2.8672.17791.49655.4149-0.36910.4596-0.34160.4102-0.22860.58320.6164-0.94390.59770.1305-0.17110.14090.3684-0.26970.756825.014162.73749.807
51.4559-0.1111-0.37920.7575-0.26310.3119-0.03550.1447-0.16860.0933-0.0680.0509-0.027-0.05340.10350.088-0.0031-0.00780.1696-0.01840.136831.040887.54355.4815
61.639-0.48620.8880.217-0.37541.7112-0.01790.30840.45510.0764-0.0884-0.0728-0.07220.0450.10630.1034-0.02360.00740.14450.11120.241832.7425107.675444.9064
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A129 - 215
2X-RAY DIFFRACTION2A216 - 472
3X-RAY DIFFRACTION3A473 - 484
4X-RAY DIFFRACTION4B129 - 147
5X-RAY DIFFRACTION5B148 - 368
6X-RAY DIFFRACTION6B369 - 484

+
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