[English] 日本語
Yorodumi
- PDB-5ikw: Crystal Structure of BMP-2-inducible kinase in complex with an In... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ikw
TitleCrystal Structure of BMP-2-inducible kinase in complex with an Indazole inhibitor
ComponentsBMP-2-inducible protein kinase
KeywordsTransferase/Transferase Inhibitor / transferase / protein kinase domain / Structural Genomics / Structural Genomics Consortium / SGC / Transferase-Transferase Inhibitor Complex
Function / homology
Function and homology information


phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding ...phosphatase regulator activity / regulation of clathrin-dependent endocytosis / AP-2 adaptor complex binding / regulation of bone mineralization / positive regulation of Notch signaling pathway / non-specific serine/threonine protein kinase / nuclear speck / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. ...BMP-2-inducible protein kinase, C-terminal / BMP-2-inducible protein kinase C-terminus / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6BU / BMP-2-inducible protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsCounago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. ...Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
Funding support Brazil, 1items
OrganizationGrant numberCountry
FAPESP2013/50724-5 Brazil
CitationJournal: To Be Published
Title: Crystal Structure of BMP-2-inducible kinase in complex with a 3-acylaminoindazole inhibitor GSK3236425A
Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / ...Authors: Counago, R.M. / Sorrell, F.J. / Krojer, T. / Savitsky, P. / Elkins, J.M. / Axtman, A. / Drewry, D. / Wells, C. / Zhang, C. / Zuercher, W. / Willson, T.M. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Arruda, P. / Gileadi, O. / Structural Genomics Consortium (SGC)
History
DepositionMar 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 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: BMP-2-inducible protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1872
Polymers34,7911
Non-polymers3961
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.957, 111.155, 164.053
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

-
Components

#1: Protein BMP-2-inducible protein kinase / BIKe


Mass: 34791.035 Da / Num. of mol.: 1 / Fragment: UNP residues 38-345 / Mutation: K320A, K321A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BMP2K, BIKE, HRIHFB2017 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9NSY1, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-6BU / N-(6-{3-[(cyclopropylsulfonyl)amino]phenyl}-1H-indazol-3-yl)cyclopropanecarboxamide


Mass: 396.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H20N4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10% (v/v) Broad MW PEG smear; 3.2 M MgCl2, 100 mM Hepes pH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→29.56 Å / Num. obs: 87521 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 52.61 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Net I/σ(I): 11.2
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 6.8 % / % possible all: 100

-
Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W9W

4w9w


Resolution: 2.41→21.75 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU R Cruickshank DPI: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.299 / SU Rfree Blow DPI: 0.21 / SU Rfree Cruickshank DPI: 0.208
RfactorNum. reflection% reflectionSelection details
Rfree0.216 747 4.93 %RANDOM
Rwork0.176 ---
obs0.178 15146 99 %-
Displacement parametersBiso mean: 53.1 Å2
Baniso -1Baniso -2Baniso -3
1--6.8587 Å20 Å20 Å2
2---3.5352 Å20 Å2
3---10.3938 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: LAST / Resolution: 2.41→21.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2317 0 28 89 2434
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012399HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.043258HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1110SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes57HARMONIC2
X-RAY DIFFRACTIONt_gen_planes363HARMONIC5
X-RAY DIFFRACTIONt_it2399HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.26
X-RAY DIFFRACTIONt_other_torsion3.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion314SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2686SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.58 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.227 140 5.27 %
Rwork0.197 2515 -
obs--97.46 %
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)
13.689-1.5349-0.6674.82680.03124.35480.07650.2284-0.5323-0.4726-0.26080.32310.3039-0.31060.18430.0085-0.0525-0.1097-0.2112-0.02460.012-0.29869.700336.4172
24.2398-1.62092.03050.13151.44490.38690.02210.03870.0543-0.2055-0.0604-0.03570.12590.08950.03820.19660.14470.02480.06250.1077-0.120711.753816.205926.1593
32.4718-0.63991.0783.2275-0.97152.85470.15180.1937-0.2688-0.1828-0.09080.11510.4274-0.058-0.061-0.0076-0.00770.0115-0.13890.0165-0.1098-0.392118.851133.082
42.7248-0.0883-1.28842.73380.62554.63070.0920.12940.06470.1208-0.0769-0.11010.24020.3986-0.01520.01620.11790.007-0.00880.0551-0.09652.751832.733626.9654
54.43530.4688-0.98070.8007-2.66940.60020.12620.2149-0.1317-0.1316-0.22270.02040.35320.26960.09650.04430.11660.0226-0.03110.0283-0.13223.848426.517227.4684
60.9128-2.7512-0.11182.7325-0.61370.8065-0.00830.0349-0.0470.08890.0353-0.05590.09090.0447-0.02690.28720.1520.10360.0713-0.0048-0.24266.986720.67577.5182
73.634-0.3277-1.68751.92130.21096.2838-0.11310.36680.0053-0.10890.10240.11360.2592-0.5420.0107-0.05920.0870.01690.04560.054-0.1885-5.487333.783414.5115
82.389-0.90140.08772.4322-0.223.79620.0130.12910.5203-0.058-0.168-0.148-0.53550.37690.155-0.03240.05290.0302-0.05480.0783-0.0222.645745.720521.7752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{A|42 - 85}
2X-RAY DIFFRACTION2{A|86 - 102}
3X-RAY DIFFRACTION3{A|103 - 151}
4X-RAY DIFFRACTION4{A|152 - 185}
5X-RAY DIFFRACTION5{A|186 - 208}
6X-RAY DIFFRACTION6{A|209 - 224}
7X-RAY DIFFRACTION7{A|225 - 287}
8X-RAY DIFFRACTION8{A|288 - 338}

+
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