[English] 日本語
Yorodumi
- PDB-6t29: Crystal structure of human calmodulin-dependent protein kinase 1D... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6t29
TitleCrystal structure of human calmodulin-dependent protein kinase 1D (CAMK1D) bound to compound 18 (CS587)
ComponentsCalcium/calmodulin-dependent protein kinase type 1D
KeywordsTRANSFERASE / Inhibitor / Complex / Kinase
Function / homology
Function and homology information


regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calcium/calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development ...regulation of granulocyte chemotaxis / positive regulation of CREB transcription factor activity / regulation of dendrite development / Ca2+/calmodulin-dependent protein kinase / positive regulation of neutrophil chemotaxis / calcium/calmodulin-dependent protein kinase activity / positive regulation of respiratory burst / positive regulation of phagocytosis / positive regulation of neuron projection development / nervous system development / calmodulin binding / inflammatory response / positive regulation of apoptotic process / protein serine kinase activity / negative regulation of apoptotic process / ATP binding / nucleus / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Chem-M8Z / Calcium/calmodulin-dependent protein kinase type 1D
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.484 Å
AuthorsKraemer, A. / Sorrell, F. / Butterworth, S. / Edwards, A.M. / Arrowsmith, C.H. / Bountra, C. / Knapp, S. / Structural Genomics Consortium (SGC)
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust202708 United Kingdom
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Highly Selective Inhibitors of Calmodulin-Dependent Kinases That Restore Insulin Sensitivity in the Diet-Induced Obesityin VivoMouse Model.
Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. ...Authors: Fromont, C. / Atzori, A. / Kaur, D. / Hashmi, L. / Greco, G. / Cabanillas, A. / Nguyen, H.V. / Jones, D.H. / Garzon, M. / Varela, A. / Stevenson, B. / Iacobini, G.P. / Lenoir, M. / Rajesh, S. / Box, C. / Kumar, J. / Grant, P. / Novitskaya, V. / Morgan, J. / Sorrell, F.J. / Redondo, C. / Kramer, A. / Harris, C.J. / Leighton, B. / Vickers, S.P. / Cheetham, S.C. / Kenyon, C. / Grabowska, A.M. / Overduin, M. / Berditchevski, F. / Weston, C.J. / Knapp, S. / Fischer, P.M. / Butterworth, S.
History
DepositionOct 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2020Group: Database references / Structure summary / Category: citation / citation_author / struct
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct.title
Revision 1.2Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Calcium/calmodulin-dependent protein kinase type 1D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,11411
Polymers42,9731
Non-polymers1,14110
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-42 kcal/mol
Surface area13410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.820, 45.640, 108.754
Angle α, β, γ (deg.)90.000, 104.183, 90.000
Int Tables number5
Space group name H-MI121
Components on special symmetry positions
IDModelComponents
11AAA-658-

HOH

21AAA-692-

HOH

-
Components

#1: Protein Calcium/calmodulin-dependent protein kinase type 1D / CaM kinase I delta / CaMKID / CaMKI-like protein kinase / CKLiK


Mass: 42972.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CAMK1D, CAMKID / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IU85, Ca2+/calmodulin-dependent protein kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-M8Z / 2-[(3~{S})-3-azanylpiperidin-1-yl]-4-[[3,5-bis(2-cyanopropan-2-yl)phenyl]amino]pyrimidine-5-carboxamide


Mass: 446.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H30N8O / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.9 / Details: 0,1M NaCit, pH 5.9 2,05M AmmSO4 0,1M Na/K tartrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.95372 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.48→55.45 Å / Num. obs: 44955 / % possible obs: 98.7 % / Redundancy: 6.3 % / CC1/2: 0.999 / Rpim(I) all: 0.026 / Net I/σ(I): 14.8
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.2 / Num. unique obs: 14295 / CC1/2: 0.883 / Rpim(I) all: 0.155 / % possible all: 98.3

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2jc6

2jc6


Resolution: 1.484→55.448 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.14 / SU ML: 0.036 / Cross valid method: FREE R-VALUE / ESU R: 0.072 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1747 2291 5.096 %
Rwork0.1355 --
all0.137 --
obs-44954 98.465 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.727 Å2-0 Å2-0.17 Å2
2---0.188 Å20 Å2
3----0.402 Å2
Refinement stepCycle: LAST / Resolution: 1.484→55.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2175 0 73 197 2445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132324
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172120
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6443148
X-RAY DIFFRACTIONr_angle_other_deg1.4161.5954918
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00623.839112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75115389
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.923158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02471
X-RAY DIFFRACTIONr_nbd_refined0.2150.2417
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.21916
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21129
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2919
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2148
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1870.214
X-RAY DIFFRACTIONr_nbd_other0.1630.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1360.220
X-RAY DIFFRACTIONr_mcbond_it1.7141.6681114
X-RAY DIFFRACTIONr_mcbond_other1.7131.6691115
X-RAY DIFFRACTIONr_mcangle_it2.3242.5121396
X-RAY DIFFRACTIONr_mcangle_other2.3232.5131397
X-RAY DIFFRACTIONr_scbond_it2.2311.9541210
X-RAY DIFFRACTIONr_scbond_other2.231.9541211
X-RAY DIFFRACTIONr_scangle_it2.8152.8131752
X-RAY DIFFRACTIONr_scangle_other2.8152.8131753
X-RAY DIFFRACTIONr_lrange_it3.53520.432595
X-RAY DIFFRACTIONr_lrange_other3.53520.4272595
X-RAY DIFFRACTIONr_rigid_bond_restr1.434444
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.484-1.5230.2051610.1573131X-RAY DIFFRACTION98.3274
1.523-1.5640.1841700.1443044X-RAY DIFFRACTION98.4078
1.564-1.610.1951760.1342945X-RAY DIFFRACTION98.3922
1.61-1.6590.1731580.1152870X-RAY DIFFRACTION97.583
1.659-1.7130.1531460.1072771X-RAY DIFFRACTION98.0834
1.713-1.7730.1581310.1042730X-RAY DIFFRACTION98.7233
1.773-1.840.1731460.1042629X-RAY DIFFRACTION98.7544
1.84-1.9150.1561170.1062549X-RAY DIFFRACTION98.7042
1.915-20.1711420.1092375X-RAY DIFFRACTION97.4826
2-2.0980.1541200.1152316X-RAY DIFFRACTION98.464
2.098-2.2110.161290.1222196X-RAY DIFFRACTION98.4752
2.211-2.3450.151160.1142099X-RAY DIFFRACTION99.4165
2.345-2.5070.146870.1141988X-RAY DIFFRACTION98.3412
2.507-2.7070.167960.1311821X-RAY DIFFRACTION98.0563
2.707-2.9650.183860.1411719X-RAY DIFFRACTION99.6687
2.965-3.3140.157780.1481552X-RAY DIFFRACTION99.4509
3.314-3.8240.213620.1471356X-RAY DIFFRACTION97.3901
3.824-4.6780.153780.1491147X-RAY DIFFRACTION99.6745
4.678-6.5920.23560.218912X-RAY DIFFRACTION98.9775

+
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