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- PDB-4uwc: Fibroblast growth factor receptor 1 kinase in complex with JK-P3 -

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Basic information

Entry
Database: PDB / ID: 4uwc
TitleFibroblast growth factor receptor 1 kinase in complex with JK-P3
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 1
KeywordsTRANSFERASE / RECEPTOR TYROSINE KINASE / TRANSFERASE INHIBITOR
Function / homology
Function and homology information


Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification ...Signaling by FGFR1 amplification mutants / negative regulation of fibroblast growth factor production / positive regulation of mitotic cell cycle DNA replication / regulation of extrinsic apoptotic signaling pathway in absence of ligand / Signaling by plasma membrane FGFR1 fusions / diphosphate metabolic process / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / cementum mineralization / positive regulation of endothelial cell chemotaxis to fibroblast growth factor / response to sodium phosphate / receptor-receptor interaction / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / auditory receptor cell development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / positive regulation of parathyroid hormone secretion / chordate embryonic development / mesenchymal cell proliferation / paraxial mesoderm development / FGFR1b ligand binding and activation / fibroblast growth factor receptor activity / branching involved in salivary gland morphogenesis / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / phosphatidylinositol-mediated signaling / outer ear morphogenesis / middle ear morphogenesis / embryonic limb morphogenesis / skeletal system morphogenesis / ureteric bud development / positive regulation of vascular endothelial cell proliferation / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / inner ear morphogenesis / midbrain development / fibroblast growth factor binding / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / PI-3K cascade:FGFR1 / regulation of cell differentiation / PI3K Cascade / epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / calcium ion homeostasis / chondrocyte differentiation / positive regulation of phospholipase C activity / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / Signaling by FGFR1 in disease / positive regulation of neuron differentiation / NCAM signaling for neurite out-growth / SH2 domain binding / Signal transduction by L1 / skeletal system development / stem cell proliferation / stem cell differentiation / positive regulation of cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / neuron migration / positive regulation of MAP kinase activity / receptor protein-tyrosine kinase / positive regulation of neuron projection development / peptidyl-tyrosine phosphorylation / cell surface receptor protein tyrosine kinase signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / neuron projection development / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding / gene expression / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / cytoplasmic vesicle / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / in utero embryonic development / positive regulation of MAPK cascade / protein autophosphorylation / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein phosphorylation / positive regulation of cell population proliferation / negative regulation of transcription by RNA polymerase II / protein homodimerization activity
Similarity search - Function
Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain ...Fibroblast growth factor receptor 1, catalytic domain / Fibroblast growth factor receptor family / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / 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-4Y0 / PROPANOIC ACID / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsBeeston, H. / Tucker, J. / Kankanala, J.
CitationJournal: Rapid Commun Mass Spectrom / Year: 2021
Title: Validation of IMS-MS as a screening tool to identify type II kinase inhibitors of FGFR1 kinase.
Authors: Beeston, H.S. / Klein, T. / Norman, R.A. / Tucker, J.A. / Anderson, M. / Ashcroft, A.E. / Holdgate, G.A.
History
DepositionAug 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Other
Revision 1.2Jun 14, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.3Jun 16, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / pdbx_refine_tls_group / struct_site
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.status_code_sf / _pdbx_refine_tls_group.selection_details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 1, 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

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,46125
Polymers70,2712
Non-polymers2,19023
Water6,107339
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,42615
Polymers35,1351
Non-polymers1,29014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: FIBROBLAST GROWTH FACTOR RECEPTOR 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,03510
Polymers35,1351
Non-polymers9009
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)207.464, 58.422, 65.946
Angle α, β, γ (deg.)90.00, 107.38, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2018-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.993, 0.111, 0.049), (0.119, 0.816, 0.566), (0.023, 0.568, -0.823)
Vector: 113.96901, -16.50727, 28.61719)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 1 / / FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / B FGF-R-1 / FMS-LIKE TYROSINE KINASE 2 ...FGFR-1 / BASIC FIBROBLAST GROWTH FACTOR RECEPTOR 1 / BFGFR / B FGF-R-1 / FMS-LIKE TYROSINE KINASE 2 / FLT-2 / N-SAM / PROTO-ONCOGENE C-FGR / FIBROBLAST GROWTH FACTOR RECEPTOR 1 KINASE


Mass: 35135.340 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 458-765 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR
References: UniProt: P11362, receptor protein-tyrosine kinase

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Non-polymers , 5 types, 362 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-4Y0 / 3,4-dimethoxy-N-(5-phenyl-1H-pyrazol-3-yl)benzamide


Mass: 323.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H17N3O3
#4: Chemical ChemComp-PPI / PROPANOIC ACID / Propionic acid


Mass: 74.079 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H6O2
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 339 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTWO MUTATIONS INTRODUCED TO IMPROVE CRYSTALLISATION AND REDUCE AGGREGATION C488A C584S

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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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growDetails: 20% PEG8000, 20% ETHYLENE GLYCOL, 0.2M AMMONIUM SULPHATE, 0.1M PCTP PH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.96→29.21 Å / Num. obs: 47605 / % possible obs: 87.8 % / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 41.84 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 16.8
Reflection shellResolution: 1.96→2.01 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 1.5 / % possible all: 41.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSVERSION MAY 10 2010data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INTERNAL FGFR1 MODEL

Resolution: 1.96→29.21 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.9309 / SU R Cruickshank DPI: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.16 / SU Rfree Blow DPI: 0.138 / SU Rfree Cruickshank DPI: 0.138
Details: DISORDERED SIDE-CHAINS WERE TRUNCATED TO THE LAST VISIBLE ATOM.
RfactorNum. reflection% reflectionSelection details
Rfree0.2058 2440 5.13 %RANDOM
Rwork0.1774 ---
obs0.1789 47602 87.56 %-
Displacement parametersBiso mean: 51.54 Å2
Baniso -1Baniso -2Baniso -3
1-7.9327 Å20 Å21.8163 Å2
2---13.2218 Å20 Å2
3---5.2892 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4600 0 141 339 5080
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014901HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.036654HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1655SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes103HARMONIC2
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it4901HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3
X-RAY DIFFRACTIONt_other_torsion15.92
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion612SEMIHARMONIC5
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_contact5827SEMIHARMONIC4
LS refinement shellResolution: 1.96→2.01 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2363 79 4.92 %
Rwork0.2223 1527 -
all0.2231 1606 -
obs--87.56 %
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)
12.2359-0.1371-0.5420.2601-0.06631.21770.1297-0.04590.1277-0.0345-0.0504-0.0134-0.1570.1828-0.0794-0.1-0.0342-0.0126-0.04610.028-0.139580.5576-2.458118.8726
22.1769-0.7833-0.04350.80520.24240.81650.1010.1977-0.150.0417-0.22210.11580.0429-0.09350.1211-0.09110.0042-0.0141-0.0889-0.0315-0.11634.20212.479713.8337
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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