[English] 日本語
Yorodumi
- PDB-7ats: The LIMK1 Kinase Domain Bound To LIJTF500127 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ats
TitleThe LIMK1 Kinase Domain Bound To LIJTF500127
ComponentsLIM domain kinase 1
KeywordsSIGNALING PROTEIN / Kinase Inhibitor Active site CFL1 Actin cytoskeleton
Function / homology
Function and homology information


positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion ...positive regulation of actin filament bundle assembly / negative regulation of ubiquitin-protein transferase activity / RHO GTPases Activate ROCKs / axon extension / Sema4D induced cell migration and growth-cone collapse / Fc-gamma receptor signaling pathway involved in phagocytosis / stress fiber assembly / RHO GTPases activate PAKs / Rho protein signal transduction / Sema3A PAK dependent Axon repulsion / positive regulation of axon extension / positive regulation of stress fiber assembly / EPHB-mediated forward signaling / heat shock protein binding / male germ cell nucleus / Regulation of actin dynamics for phagocytic cup formation / lamellipodium / nervous system development / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / neuron projection / protein kinase activity / nuclear speck / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / signal transduction / ATP binding / membrane / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily ...LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, 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
Similarity search - Domain/homology
Chem-RXQ / LIM domain kinase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMathea, S. / Chatterjee, D. / Preuss, F. / Yamamoto, S. / Tawada, M. / Nomura, I. / Takagi, T. / Ahmed, M. / Little, W. / Mueller-Knapp, S. / Knapp, S.
CitationJournal: To Be Published
Title: The LIMK1 Kinase Domain Bound To LIJTF500127
Authors: Mathea, S. / Chatterjee, D. / Preuss, F. / Yamamoto, S. / Tawada, M. / Nomura, I. / Takagi, T. / Ahmed, M. / Little, W. / Mueller-Knapp, S. / Knapp, S.
History
DepositionOct 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LIM domain kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5192
Polymers35,9951
Non-polymers5241
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Methodgel filtration
Unit cell
Length a, b, c (Å)81.096, 81.096, 173.953
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

-
Components

#1: Protein LIM domain kinase 1 / LIMK-1


Mass: 35994.773 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIMK1, LIMK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P53667, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-RXQ / N-[3-[5-(4-Chlorophenyl)-1H-pyrrolo[2,3-b]pyridine-3-carbonyl]-2,4-difluorophenyl]benzenesulfonamide / N-[3-[[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl]-2,4-bis(fluoranyl)phenyl]benzenesulfonamide / LIJTF500127


Mass: 523.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H16ClF2N3O3S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 0.1 M bis-tris-propane pH 7.5 0.2 M potassium thiocyanate 10% ethylene glycol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.9999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.8→44.71 Å / Num. obs: 8956 / % possible obs: 100 % / Redundancy: 4.7 % / Biso Wilson estimate: 94.95 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 16.5
Reflection shellResolution: 2.8→2.95 Å / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1255

-
Processing

Software
NameVersionClassification
REFMAC7.0.053refinement
PHENIX1.18.2_3874refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NXC

5nxc


Resolution: 2.8→44.71 Å / SU ML: 0.2732 / Cross valid method: FREE R-VALUE / σ(F): 1.57 / Phase error: 38.678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3122 449 5.04 %
Rwork0.2478 8454 -
obs0.2511 8903 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 87.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1883 0 36 0 1919
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01141975
X-RAY DIFFRACTIONf_angle_d1.34262718
X-RAY DIFFRACTIONf_chiral_restr0.0699309
X-RAY DIFFRACTIONf_plane_restr0.0093390
X-RAY DIFFRACTIONf_dihedral_angle_d7.4702319
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.210.34681520.27332717X-RAY DIFFRACTION99.97
3.21-4.040.32581440.27262774X-RAY DIFFRACTION99.93
4.04-44.710.3021530.23512963X-RAY DIFFRACTION99.9
Refinement TLS params.Method: refined / Origin x: -12.2841886409 Å / Origin y: 32.145028667 Å / Origin z: -7.88985935969 Å
111213212223313233
T0.635629711395 Å2-0.0281263147259 Å2-0.0270613761225 Å2-0.693957867867 Å2-0.017309484848 Å2--0.579963937761 Å2
L1.63731232605 °20.880219880356 °2-0.305160095579 °2-1.17013150677 °20.45108340405 °2--0.588301841079 °2
S0.056830386854 Å °0.171652045231 Å °-0.20553232865 Å °-0.0629114457101 Å °0.0424772208982 Å °0.00431980323005 Å °0.0522710041761 Å °0.118832730826 Å °0.000189370033369 Å °
Refinement TLS groupSelection details: all

+
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