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- PDB-7btt: A X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain -

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Basic information

Entry
Database: PDB / ID: 7btt
TitleA X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain
ComponentsALK tyrosine kinase receptor
KeywordsTRANSFERASE / Kinase / ATP Binding / inhibitor / Complex
Function / homology
Function and homology information


ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway ...ASP-3026-resistant ALK mutants / NVP-TAE684-resistant ALK mutants / alectinib-resistant ALK mutants / brigatinib-resistant ALK mutants / ceritinib-resistant ALK mutants / crizotinib-resistant ALK mutants / lorlatinib-resistant ALK mutants / MDK and PTN in ALK signaling / receptor signaling protein tyrosine kinase activator activity / regulation of dopamine receptor signaling pathway / response to environmental enrichment / ALK mutants bind TKIs / swimming behavior / positive regulation of dendrite development / regulation of neuron differentiation / Signaling by ALK / adult behavior / neuron development / negative regulation of lipid catabolic process / phosphorylation / peptidyl-tyrosine autophosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / energy homeostasis / transmembrane receptor protein tyrosine kinase activity / hippocampus development / receptor protein-tyrosine kinase / Signaling by ALK fusions and activated point mutants / heparin binding / positive regulation of NF-kappaB transcription factor activity / regulation of cell population proliferation / protein tyrosine kinase activity / regulation of apoptotic process / protein autophosphorylation / receptor complex / signal transduction / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane
Similarity search - Function
Glycine rich protein / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : ...Glycine rich protein / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Tyrosine-protein kinase, receptor class II, conserved site / Receptor tyrosine kinase class II signature. / : / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Concanavalin A-like lectin/glucanase domain superfamily / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-F8R / ALK tyrosine kinase receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsYun, C.H. / Zhu, S.J.
CitationJournal: To Be Published
Title: A X-ray cocrystal structure of XMU-MP-5 bound to the ALK kinase domain
Authors: Yun, C.H. / Zhu, S.J.
History
DepositionApr 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: ALK tyrosine kinase receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4982
Polymers35,9341
Non-polymers5641
Water2,828157
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13990 Å2
Unit cell
Length a, b, c (Å)51.525, 57.441, 105.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein ALK tyrosine kinase receptor / Anaplastic lymphoma kinase


Mass: 35934.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q9UM73, receptor protein-tyrosine kinase
#2: Chemical ChemComp-F8R / 2-(dimethylamino)-1-[5-methoxy-6-[[4-[(2-propan-2-ylsulfonylphenyl)amino]-5H-pyrrolo[3,2-d]pyrimidin-2-yl]amino]-2,3-dihydroindol-1-yl]ethanone


Mass: 563.671 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H33N7O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Sodium chloride, 25% w/v Polyethylene glycol 3,350, 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97775 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97775 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 26903 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 31.95 Å2 / CC1/2: 0.981 / Net I/σ(I): 10.8
Reflection shellResolution: 1.86→1.9 Å / Num. unique obs: 1760 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L9P

3l9p


Resolution: 1.86→46.29 Å / SU ML: 0.2426 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1458
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 1353 5.04 %0.05
Rwork0.1867 ---
obs0.1879 26858 99.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.87 Å2
Refinement stepCycle: LAST / Resolution: 1.86→46.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2385 0 40 157 2582
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00742497
X-RAY DIFFRACTIONf_angle_d0.93823394
X-RAY DIFFRACTIONf_chiral_restr0.0589360
X-RAY DIFFRACTIONf_plane_restr0.0063439
X-RAY DIFFRACTIONf_dihedral_angle_d19.17621496
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.920.35021350.28742462X-RAY DIFFRACTION96.9
1.92-20.29841280.23642515X-RAY DIFFRACTION99.92
2-2.090.28251400.22412497X-RAY DIFFRACTION99.58
2.09-2.20.25261240.20352553X-RAY DIFFRACTION99.55
2.2-2.340.25921490.20652534X-RAY DIFFRACTION99.74
2.34-2.520.2341320.18992524X-RAY DIFFRACTION99.55
2.52-2.780.23021450.18742555X-RAY DIFFRACTION99.74
2.78-3.180.21521330.1852570X-RAY DIFFRACTION99.59
3.18-40.18171280.16652604X-RAY DIFFRACTION99.24
4-46.290.16431390.17612691X-RAY DIFFRACTION97.96

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