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- PDB-5u6b: Structure of the Axl kinase domain in complex with a macrocyclic ... -

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Basic information

Entry
Database: PDB / ID: 5u6b
TitleStructure of the Axl kinase domain in complex with a macrocyclic inhibitor
ComponentsTyrosine-protein kinase receptor UFO
KeywordsTransferase/Transferase Inhibitor / Kinase Inhibitor Complex / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


forebrain cell migration / positive regulation of natural killer cell differentiation / negative regulation of lymphocyte activation / cellular response to interferon-alpha / positive regulation of pinocytosis / negative regulation of macrophage cytokine production / positive regulation of cytokine-mediated signaling pathway / neutrophil clearance / natural killer cell differentiation / dendritic cell differentiation ...forebrain cell migration / positive regulation of natural killer cell differentiation / negative regulation of lymphocyte activation / cellular response to interferon-alpha / positive regulation of pinocytosis / negative regulation of macrophage cytokine production / positive regulation of cytokine-mediated signaling pathway / neutrophil clearance / natural killer cell differentiation / dendritic cell differentiation / : / secretion by cell / positive regulation of viral life cycle / negative regulation of dendritic cell apoptotic process / erythrocyte homeostasis / ovulation cycle / phosphatidylserine binding / myosin heavy chain binding / vagina development / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / response to axon injury / blood vessel remodeling / animal organ regeneration / vascular endothelial growth factor receptor signaling pathway / phosphatidylinositol 3-kinase binding / phagocytosis / cell maturation / transmembrane receptor protein tyrosine kinase activity / substrate adhesion-dependent cell spreading / phosphatidylinositol 3-kinase/protein kinase B signal transduction / establishment of localization in cell / neuron migration / receptor protein-tyrosine kinase / cellular response to hydrogen peroxide / platelet activation / VEGFA-VEGFR2 Pathway / cell surface receptor protein tyrosine kinase signaling pathway / cell migration / actin cytoskeleton / virus receptor activity / nervous system development / spermatogenesis / protein tyrosine kinase activity / neuron apoptotic process / cellular response to lipopolysaccharide / negative regulation of neuron apoptotic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / inflammatory response / symbiont entry into host cell / phosphorylation / innate immune response / intracellular membrane-bounded organelle / negative regulation of apoptotic process / cell surface / signal transduction / extracellular space / extracellular exosome / ATP binding / plasma membrane
Similarity search - Function
Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype ...Immunoglobulin domain / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / 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-7YS / Tyrosine-protein kinase receptor UFO
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.84 Å
AuthorsGajiwala, K.S. / Grodsky, N.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: The Axl kinase domain in complex with a macrocyclic inhibitor offers first structural insights into an active TAM receptor kinase.
Authors: Gajiwala, K.S. / Grodsky, N. / Bolanos, B. / Feng, J. / Ferre, R. / Timofeevski, S. / Xu, M. / Murray, B.W. / Johnson, T.W. / Stewart, A.
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 4, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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: Tyrosine-protein kinase receptor UFO
B: Tyrosine-protein kinase receptor UFO
C: Tyrosine-protein kinase receptor UFO
D: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,3248
Polymers139,4804
Non-polymers1,8444
Water0
1
A: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3312
Polymers34,8701
Non-polymers4611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3312
Polymers34,8701
Non-polymers4611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3312
Polymers34,8701
Non-polymers4611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tyrosine-protein kinase receptor UFO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3312
Polymers34,8701
Non-polymers4611
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.680, 100.704, 81.921
Angle α, β, γ (deg.)90.00, 93.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Tyrosine-protein kinase receptor UFO / AXL oncogene


Mass: 34869.988 Da / Num. of mol.: 4 / Fragment: UNP residues 514-818
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AXL, UFO / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P30530, receptor protein-tyrosine kinase
#2: Chemical
ChemComp-7YS / (10R)-7-amino-11-chloro-12-fluoro-1-(2-hydroxyethyl)-3,10,16-trimethyl-16,17-dihydro-1H-8,4-(azeno)pyrazolo[4,3-h][2,5,11]benzoxadiazacyclotetradecin-15(10H)-one


Mass: 460.889 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H22ClFN6O3

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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: 2.41 Å3/Da / Density % sol: 48.96 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 1.2 microL of the protein-ligand complex (1:3 ratio of protein:ligand) and 1.2 microL of the reservoir solution (0.1 M Tris, pH 8.5, 0.2 M MgCl2, 30 % (w/v) PEG-4000, 1-2 % (v/v) 1-butanol).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.84→63 Å / Num. obs: 31278 / % possible obs: 99.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.19 Å2 / Rsym value: 0.095 / Net I/σ(I): 12
Reflection shellResolution: 2.84→2.99 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4542 / % possible all: 99.8

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementResolution: 2.84→59.81 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.88 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.351
RfactorNum. reflection% reflectionSelection details
Rfree0.239 759 4.84 %RANDOM
Rwork0.211 ---
obs0.212 31142 99.3 %-
Displacement parametersBiso mean: 56.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.1518 Å20 Å2-1.5426 Å2
2--11.9473 Å20 Å2
3----10.7955 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: 1 / Resolution: 2.84→59.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8922 0 128 0 9050
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0099238HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0912478HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3280SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes228HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1420HARMONIC5
X-RAY DIFFRACTIONt_it9238HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.36
X-RAY DIFFRACTIONt_other_torsion22.31
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1154SEMIHARMONIC5
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_contact10404SEMIHARMONIC4
LS refinement shellResolution: 2.84→2.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.288 146 5.09 %
Rwork0.249 2722 -
all0.251 2868 -
obs--99.83 %

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