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- PDB-2fgi: CRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1... -

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Basic information

Entry
Database: PDB / ID: 2fgi
TitleCRYSTAL STRUCTURE OF THE TYROSINE KINASE DOMAIN OF FGF RECEPTOR 1 IN COMPLEX WITH INHIBITOR PD173074
ComponentsPROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1)
KeywordsTRANSFERASE / PROTEIN KINASE / TYROSINE-PROTEIN KINASE / ATP-BINDING / PHOSPHORYLATION / 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 / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process ...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 / regulation of phosphate transport / regulation of lateral mesodermal cell fate specification / FGFR1c and Klotho ligand binding and activation / vitamin D3 metabolic process / cementum mineralization / positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway / regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling / receptor-receptor interaction / response to sodium phosphate / auditory receptor cell development / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / Epithelial-Mesenchymal Transition (EMT) during gastrulation / chordate embryonic development / positive regulation of parathyroid hormone secretion / mesenchymal cell proliferation / paraxial mesoderm development / regulation of postsynaptic density assembly / FGFR1b ligand binding and activation / Signaling by activated point mutants of FGFR1 / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / branching involved in salivary gland morphogenesis / Phospholipase C-mediated cascade: FGFR1 / positive regulation of phospholipase activity / lung-associated mesenchyme development / cell projection assembly / outer ear morphogenesis / embryonic limb morphogenesis / positive regulation of vascular endothelial cell proliferation / positive regulation of endothelial cell chemotaxis / skeletal system morphogenesis / positive regulation of mesenchymal cell proliferation / middle ear morphogenesis / ureteric bud development / cardiac muscle cell proliferation / inner ear morphogenesis / phosphatidylinositol-mediated signaling / PI-3K cascade:FGFR1 / midbrain development / positive regulation of stem cell proliferation / Formation of paraxial mesoderm / fibroblast growth factor binding / regulation of cell differentiation / PI3K Cascade / cellular response to fibroblast growth factor stimulus / positive regulation of blood vessel endothelial cell migration / fibroblast growth factor receptor signaling pathway / epithelial to mesenchymal transition / chondrocyte differentiation / calcium ion homeostasis / SHC-mediated cascade:FGFR1 / cell maturation / positive regulation of cardiac muscle cell proliferation / FRS-mediated FGFR1 signaling / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / positive regulation of MAP kinase activity / positive regulation of neuron differentiation / SH2 domain binding / Signal transduction by L1 / stem cell proliferation / skeletal system development / positive regulation of cell differentiation / stem cell differentiation / sensory perception of sound / Negative regulation of FGFR1 signaling / placental growth factor receptor activity / insulin receptor activity / vascular endothelial growth factor receptor activity / hepatocyte growth factor receptor activity / macrophage colony-stimulating factor receptor activity / platelet-derived growth factor alpha-receptor activity / platelet-derived growth factor beta-receptor activity / stem cell factor receptor activity / boss receptor activity / protein tyrosine kinase collagen receptor activity / brain-derived neurotrophic factor receptor activity / transmembrane-ephrin receptor activity / GPI-linked ephrin receptor activity / epidermal growth factor receptor activity / fibroblast growth factor receptor activity / insulin-like growth factor receptor activity / receptor protein-tyrosine kinase / peptidyl-tyrosine phosphorylation / positive regulation of neuron projection development / neuron migration / neuron projection development / Constitutive Signaling by Aberrant PI3K in Cancer / MAPK cascade / cell migration / PIP3 activates AKT signaling / heparin binding
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 ...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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Phosphorylase Kinase; domain 1 / Ig-like domain profile. / Immunoglobulin-like domain / Phosphorylase Kinase; domain 1 / Immunoglobulin-like domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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-PD1 / Fibroblast growth factor receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsMohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R.
CitationJournal: EMBO J. / Year: 1998
Title: Crystal structure of an angiogenesis inhibitor bound to the FGF receptor tyrosine kinase domain.
Authors: Mohammadi, M. / Froum, S. / Hamby, J.M. / Schroeder, M.C. / Panek, R.L. / Lu, G.H. / Eliseenkova, A.V. / Green, D. / Schlessinger, J. / Hubbard, S.R.
History
DepositionSep 15, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1)
B: PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6654
Polymers70,6172
Non-polymers1,0472
Water3,441191
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)208.790, 57.380, 66.180
Angle α, β, γ (deg.)90.00, 107.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9944, -0.09773, 0.04029), (-0.10388, 0.83277, -0.54379), (0.01959, -0.54493, -0.83826)
Vector: 72.518, 12.243, 28.159)

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Components

#1: Protein PROTEIN (FIBROBLAST GROWTH FACTOR (FGF) RECEPTOR 1) / FGFR1K


Mass: 35308.613 Da / Num. of mol.: 2 / Fragment: TYROSINE KINASE DOMAIN / Mutation: L457V, C488A, C584S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Cellular location: CYTOPLASM / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P11362, EC: 2.7.1.112
#2: Chemical ChemComp-PD1 / 1-TERT-BUTYL-3-[6-(3,5-DIMETHOXY-PHENYL)-2-(4-DIETHYLAMINO-BUTYLAMINO)-PYRIDO[2,3-D]PYRIMIDIN-7-YL]-UREA / PD 173074


Mass: 523.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H41N7O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.68 Å3/Da / Density % sol: 54 %
Crystal growpH: 6.5
Details: 16% PEG 10000, 0.3 M (NH4)2SO4, 100 MM BIS-TRIS, PH 6.5, 5% ETHYLENE GLYCOL
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop / Details: Mohammadi, M., (1996) Cell, 86, 577.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-50 mg/mlprotein1drop
210 mMTris-HCl1drop
310 mM1dropNaCl
42 mMdithiothreitol1drop
516 %PEG100001reservoir
60.3 Mammonium sulfate1reservoir
75 %ethylene glycol1reservoir
8100 mMbis-Tris1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Aug 27, 1997 / Details: YALE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 24664 / % possible obs: 94.5 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 12.4
Reflection
*PLUS
Num. measured all: 93535
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.252

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Processing

Software
NameVersionClassification
X-PLOR3.816refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→6 Å / Rfactor Rfree error: 0.0081 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1185 4.3 %RANDOM
Rwork0.204 ---
obs0.204 23530 85.6 %-
Displacement parametersBiso mean: 45.9 Å2
Baniso -1Baniso -2Baniso -3
1-9.8 Å20 Å24.14 Å2
2---20.01 Å20 Å2
3---10.21 Å2
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 76 191 4573
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.36
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d22.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.08
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.571
X-RAY DIFFRACTIONx_mcangle_it2.681.5
X-RAY DIFFRACTIONx_scbond_it2.741.5
X-RAY DIFFRACTIONx_scangle_it4.252
Refine LS restraints NCSNCS model details: UNRESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAMCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3TOPHCSDX.MISC
Software
*PLUS
Name: X-PLOR / Version: 3.816 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / σ(F): 2 / % reflection Rfree: 4.3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 45.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg22.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.08
X-RAY DIFFRACTIONx_mcbond_it1
X-RAY DIFFRACTIONx_scbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it1.5
X-RAY DIFFRACTIONx_scangle_it2

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