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- PDB-6tu9: The ROR1 Pseudokinase Domain Bound To Ponatinib -

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Basic information

Entry
Database: PDB / ID: 6tu9
TitleThe ROR1 Pseudokinase Domain Bound To Ponatinib
ComponentsInactive tyrosine-protein kinase transmembrane receptor ROR1
KeywordsSIGNALING PROTEIN / Receptor Transmembrane Kinase Pseudokinase Small-molecule inhibitor
Function / homology
Function and homology information


WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / stress fiber / cell surface receptor protein tyrosine kinase signaling pathway / axon terminus / transmembrane receptor protein tyrosine kinase activity ...WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / Wnt receptor activity / Wnt-protein binding / astrocyte development / inner ear development / coreceptor activity / stress fiber / cell surface receptor protein tyrosine kinase signaling pathway / axon terminus / transmembrane receptor protein tyrosine kinase activity / sensory perception of sound / positive regulation of neuron projection development / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / cell surface / ATP binding / plasma membrane / cytoplasm
Similarity search - Function
Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. ...Tyrosine-protein kinase, receptor ROR / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Kringle-like fold / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / 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-0LI / Inactive tyrosine-protein kinase transmembrane receptor ROR1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsMathea, S. / Preuss, F. / Chatterjee, D. / Niininen, W. / Ungureanu, D. / Shin, D. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Knapp, S.
CitationJournal: Mol.Cell / Year: 2020
Title: Structural Insights into Pseudokinase Domains of Receptor Tyrosine Kinases.
Authors: Sheetz, J.B. / Mathea, S. / Karvonen, H. / Malhotra, K. / Chatterjee, D. / Niininen, W. / Perttila, R. / Preuss, F. / Suresh, K. / Stayrook, S.E. / Tsutsui, Y. / Radhakrishnan, R. / ...Authors: Sheetz, J.B. / Mathea, S. / Karvonen, H. / Malhotra, K. / Chatterjee, D. / Niininen, W. / Perttila, R. / Preuss, F. / Suresh, K. / Stayrook, S.E. / Tsutsui, Y. / Radhakrishnan, R. / Ungureanu, D. / Knapp, S. / Lemmon, M.A.
History
DepositionJan 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _citation.country ..._chem_comp.name / _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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Aug 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Inactive tyrosine-protein kinase transmembrane receptor ROR1
B: Inactive tyrosine-protein kinase transmembrane receptor ROR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9634
Polymers70,8972
Non-polymers1,0652
Water1,69394
1
A: Inactive tyrosine-protein kinase transmembrane receptor ROR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9812
Polymers35,4491
Non-polymers5331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inactive tyrosine-protein kinase transmembrane receptor ROR1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9812
Polymers35,4491
Non-polymers5331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.290, 85.969, 72.980
Angle α, β, γ (deg.)90.000, 91.045, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Inactive tyrosine-protein kinase transmembrane receptor ROR1 / Neurotrophic tyrosine kinase / receptor-related 1


Mass: 35448.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ROR1, NTRKR1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q01973
#2: Chemical ChemComp-0LI / 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide / Ponatinib


Mass: 532.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H27F3N6O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 0.1 M MES pH 7.2, 12% PEG20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Dec 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.94→42.98 Å / Num. obs: 49088 / % possible obs: 98.9 % / Redundancy: 5 % / Biso Wilson estimate: 34.75 Å2 / CC1/2: 1 / Net I/σ(I): 8
Reflection shellResolution: 1.94→1.99 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 3246 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GT4

4gt4


Resolution: 1.94→42.98 Å / SU ML: 0.2604 / Cross valid method: FREE R-VALUE / σ(F): 1.55 / Phase error: 30.6522
RfactorNum. reflection% reflection
Rfree0.2414 2583 5.27 %
Rwork0.2088 --
obs0.2105 49010 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.53 Å2
Refinement stepCycle: LAST / Resolution: 1.94→42.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4000 0 78 94 4172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734196
X-RAY DIFFRACTIONf_angle_d0.84685711
X-RAY DIFFRACTIONf_chiral_restr0.0551621
X-RAY DIFFRACTIONf_plane_restr0.0052780
X-RAY DIFFRACTIONf_dihedral_angle_d17.5011628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.94-1.980.42041510.38592518X-RAY DIFFRACTION98.12
1.98-2.020.39661310.34522526X-RAY DIFFRACTION96.83
2.02-2.060.35651320.3152558X-RAY DIFFRACTION97.89
2.06-2.110.3331570.29162564X-RAY DIFFRACTION99.31
2.11-2.160.32351330.25262626X-RAY DIFFRACTION99.03
2.16-2.220.31021530.22892544X-RAY DIFFRACTION99.23
2.22-2.290.24581520.21922575X-RAY DIFFRACTION99.06
2.29-2.360.28271400.21352617X-RAY DIFFRACTION99.07
2.36-2.440.26491150.20822581X-RAY DIFFRACTION99.23
2.44-2.540.28951490.21192584X-RAY DIFFRACTION99.35
2.54-2.660.25941300.21092597X-RAY DIFFRACTION99.09
2.66-2.80.26121560.2142560X-RAY DIFFRACTION98.69
2.8-2.970.2531590.21192553X-RAY DIFFRACTION97.62
2.97-3.20.28421380.21372615X-RAY DIFFRACTION99.64
3.2-3.520.2361520.20472585X-RAY DIFFRACTION99.2
3.52-4.030.22511410.19092588X-RAY DIFFRACTION98.59
4.03-5.080.17571540.16552608X-RAY DIFFRACTION99
5.08-42.980.18851400.19782628X-RAY DIFFRACTION97.77
Refinement TLS params.Method: refined / Origin x: -14.0379918679 Å / Origin y: 29.2720116605 Å / Origin z: -18.6884529476 Å
111213212223313233
T0.236601956962 Å20.0126234360081 Å2-0.0491815006731 Å2-0.252862743666 Å2-0.0190399180859 Å2--0.324257993401 Å2
L0.473690050931 °20.368507819508 °2-0.792506941589 °2-0.734275156758 °2-0.458914883204 °2--1.25643703953 °2
S0.0342589907782 Å °0.0166681913035 Å °-0.0100070713615 Å °0.00901323962452 Å °-0.0319209419436 Å °-0.00951247094593 Å °-0.0463472374387 Å °-0.0137950753964 Å °-0.00428331247484 Å °
Refinement TLS groupSelection details: all

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