[English] 日本語
Yorodumi
- PDB-4yzm: Humanized Roco4 bound to LRRK2-In1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4yzm
TitleHumanized Roco4 bound to LRRK2-In1
ComponentsProbable serine/threonine-protein kinase roco4
KeywordsTRANSFERASE / Roco-Protein / Kinase / LRRK2 / Inhibitor
Function / homology
Function and homology information


sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity ...sorocarp stalk development / Regulation of necroptotic cell death / phototaxis / mitochondrial electron transport, NADH to ubiquinone / response to reactive oxygen species / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / GTP binding / signal transduction / mitochondrion / ATP binding / cytosol / cytoplasm
Similarity search - Function
C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / : / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat ...C-terminal of Roc (COR) domain / C-terminal of Roc, COR, domain / Ras of Complex, Roc, domain of DAPkinase / Roc domain profile. / Roc domain / : / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Trp-Asp (WD) repeats circular profile. / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / WD40 repeats / Phosphorylase Kinase; domain 1 / WD40 repeat / Phosphorylase Kinase; domain 1 / WD40-repeat-containing domain superfamily / Winged helix-like DNA-binding domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-4K4 / Probable serine/threonine-protein kinase roco4
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGilsbach, B.K. / Messias, A.C. / Ito, G. / Sattler, M. / Alessi, D.R. / Wittinghofer, A. / Kortholt, A.
CitationJournal: J.Med.Chem. / Year: 2015
Title: Structural Characterization of LRRK2 Inhibitors.
Authors: Gilsbach, B.K. / Messias, A.C. / Ito, G. / Sattler, M. / Alessi, D.R. / Wittinghofer, A. / Kortholt, A.
History
DepositionMar 25, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Jan 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable serine/threonine-protein kinase roco4
B: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2876
Polymers65,0972
Non-polymers1,1904
Water64936
1
A: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1433
Polymers32,5491
Non-polymers5952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable serine/threonine-protein kinase roco4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1433
Polymers32,5491
Non-polymers5952
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.030, 89.070, 177.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Probable serine/threonine-protein kinase roco4 / Ras of complex proteins and C-terminal of roc 4


Mass: 32548.508 Da / Num. of mol.: 2 / Fragment: UNP residues 1019-1292
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Gene: roco4, DDB_G0288251 / Plasmid: pGEX4T1 NTev / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6XHB2, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-4K4 / 2-[(2-methoxy-4-{[4-(4-methylpiperazin-1-yl)piperidin-1-yl]carbonyl}phenyl)amino]-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one


Mass: 570.685 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H38N8O3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 mM 1,3-bis(tris (hydroxymethyl)methylamino)propane (pH 8.5), 200 mM Na/K tartrate, 11% (m/v) PEG 3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97889 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Sep 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 3→44.43 Å / Num. obs: 13688 / % possible obs: 99.3 % / Redundancy: 2.9 % / Net I/σ(I): 10.62
Reflection shellResolution: 3→3.5 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 4.36 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4f0f

4f0f


Resolution: 3→44.43 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.843 / SU B: 38.046 / SU ML: 0.345 / Cross valid method: THROUGHOUT / ESU R Free: 0.491 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2819 719 5 %RANDOM
Rwork0.19556 ---
obs0.19982 13688 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.501 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→44.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4203 0 86 36 4325
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.024512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9432.0036108
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2715534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.124.271199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.16315792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8971524
X-RAY DIFFRACTIONr_chiral_restr0.1420.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213397
X-RAY DIFFRACTIONr_gen_planes_other
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
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 46 -
Rwork0.263 886 -
obs--99.68 %
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)
11.42870.78-0.65151.6092-0.22031.57440.1326-0.15860.01920.2589-0.1101-0.03030.08530.037-0.02260.06750.0043-0.00560.0923-0.02190.0828-20.83660.0293-31.7111
21.44130.28280.30381.54530.35712.07930.1503-0.0382-0.10190.2039-0.0977-0.0238-0.1111-0.0663-0.05260.0610.00150.01030.05670.00610.0645-1.033941.8263-15.1241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

+
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