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- PDB-5qin: TGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN IN COMPLEX WITH N- {4-[3-(... -

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Basic information

Entry
Database: PDB / ID: 5qin
TitleTGF-BETA RECEPTOR TYPE 2 KINASE DOMAIN IN COMPLEX WITH N- {4-[3-(6-METHOXYPYRIDIN-3-YL)-1H-PYRROLO[3,2-B]PYRIDIN-2- YL]PYRIDIN-2-YL}ACETAMIDE
ComponentsTGF-beta receptor type-2
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / KINASE DOMAIN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE
Function / homology
Function and homology information


positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / activin receptor activity / miRNA transport / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / Langerhans cell differentiation / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / secondary palate development / cardiac left ventricle morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / endocardial cushion fusion / positive regulation of T cell tolerance induction / membranous septum morphogenesis / lung lobe morphogenesis / positive regulation of NK T cell differentiation / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / SMAD protein signal transduction / regulation of stem cell differentiation / glycosaminoglycan binding / kinase activator activity / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / aortic valve morphogenesis / lens development in camera-type eye / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / trachea formation / artery morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / activation of protein kinase activity / roof of mouth development / positive regulation of epithelial cell migration / blood vessel development / heart looping / outflow tract morphogenesis / SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition / vasculogenesis / positive regulation of epithelial to mesenchymal transition / gastrulation / Notch signaling pathway / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / caveola / brain development / cellular response to growth factor stimulus / positive regulation of angiogenesis / UCH proteinases / positive regulation of reactive oxygen species metabolic process / heart development / regulation of cell population proliferation / regulation of gene expression / in utero embryonic development / molecular adaptor activity / receptor complex / response to xenobiotic stimulus / membrane raft / phosphorylation / external side of plasma membrane / apoptotic process / positive regulation of cell population proliferation / extracellular space / extracellular region / ATP binding / membrane / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / 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 / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-J2V / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.57 Å
AuthorsSheriff, S.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: Discovery of 4-Azaindole Inhibitors of TGF beta RI as Immuno-oncology Agents.
Authors: Zhang, Y. / Zhao, Y. / Tebben, A.J. / Sheriff, S. / Ruzanov, M. / Fereshteh, M.P. / Fan, Y. / Lippy, J. / Swanson, J. / Ho, C.P. / Wautlet, B.S. / Rose, A. / Parrish, K. / Yang, Z. / ...Authors: Zhang, Y. / Zhao, Y. / Tebben, A.J. / Sheriff, S. / Ruzanov, M. / Fereshteh, M.P. / Fan, Y. / Lippy, J. / Swanson, J. / Ho, C.P. / Wautlet, B.S. / Rose, A. / Parrish, K. / Yang, Z. / Donnell, A.F. / Zhang, L. / Fink, B.E. / Vite, G.D. / Augustine-Rauch, K. / Fargnoli, J. / Borzilleri, R.M.
History
DepositionAug 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2018Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 12, 2021Group: Derived calculations / Structure summary
Category: pdbx_deposit_group / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_deposit_group.group_type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._pdbx_deposit_group.group_type / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,3164
Polymers35,8411
Non-polymers4763
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.450, 75.110, 75.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGF-beta receptor type-2 / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TbetaR-II


Mass: 35840.680 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 237-549
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Plasmid: PFASTBAC1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm)
References: UniProt: P37173, receptor protein serine/threonine kinase
#2: Chemical ChemComp-J2V / N-{4-[3-(6-methoxypyridin-3-yl)-1H-pyrrolo[3,2-b]pyridin-2-yl]pyridin-2-yl}acetamide


Mass: 359.381 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17N5O2
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 23%(w/v) PEG3350, 3%(v/v) glcyerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→40.99 Å / Num. obs: 51988 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 26.51 Å2 / Rsym value: 0.039 / Net I/σ(I): 21.3
Reflection shellResolution: 1.57→1.76 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.387 / Rejects: 0 / % possible all: 99.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimlessdata scaling
AMoREphasing
BUSTER2.11.6refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TZM

3tzm


Resolution: 1.57→40.99 Å / Cor.coef. Fo:Fc: 0.9613 / Cor.coef. Fo:Fc free: 0.9576 / SU R Cruickshank DPI: 0.073 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.075 / SU Rfree Blow DPI: 0.072 / SU Rfree Cruickshank DPI: 0.071
RfactorNum. reflection% reflectionSelection details
Rfree0.2026 2530 4.92 %RANDOM
Rwork0.1869 ---
obs0.1877 51413 99.69 %-
Displacement parametersBiso max: 142.61 Å2 / Biso mean: 30.22 Å2 / Biso min: 14.64 Å2
Baniso -1Baniso -2Baniso -3
1--2.7085 Å20 Å20 Å2
2---0.1103 Å20 Å2
3---2.8188 Å2
Refine analyzeLuzzati coordinate error obs: 0.183 Å
Refinement stepCycle: final / Resolution: 1.57→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2275 0 34 218 2527
Biso mean--24.56 38.87 -
Num. residues----295
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d806SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes50HARMONIC2
X-RAY DIFFRACTIONt_gen_planes387HARMONIC5
X-RAY DIFFRACTIONt_it2392HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion312SEMIHARMONIC5
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_contact2928SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2392HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg3262HARMONIC21.03
X-RAY DIFFRACTIONt_omega_torsion3.76
X-RAY DIFFRACTIONt_other_torsion14.94
LS refinement shellResolution: 1.57→1.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 189 5.14 %
Rwork0.2131 3487 -
all0.2158 3676 -
obs--99.69 %

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