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- PDB-1gjo: The FGFr2 tyrosine kinase domain -

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Basic information

Entry
Database: PDB / ID: 1gjo
TitleThe FGFr2 tyrosine kinase domain
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 2
KeywordsTRANSFERASE / TYROSINE KINASE / FGFR2 RECEPTOR
Function / homology
Function and homology information


Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development ...Signaling by FGFR2 amplification mutants / Signaling by FGFR2 fusions / fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow cell / fibroblast growth factor receptor signaling pathway involved in hemopoiesis / fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow / lateral sprouting from an epithelium / mammary gland bud formation / branch elongation involved in salivary gland morphogenesis / mesenchymal cell differentiation involved in lung development / squamous basal epithelial stem cell differentiation involved in prostate gland acinus development / lacrimal gland development / otic vesicle formation / prostate gland morphogenesis / bud elongation involved in lung branching / regulation of smooth muscle cell differentiation / regulation of morphogenesis of a branching structure / epithelial cell proliferation involved in salivary gland morphogenesis / orbitofrontal cortex development / branching involved in labyrinthine layer morphogenesis / morphogenesis of embryonic epithelium / mesenchymal cell proliferation involved in lung development / epidermis morphogenesis / branching morphogenesis of a nerve / lung-associated mesenchyme development / gland morphogenesis / embryonic organ morphogenesis / branching involved in salivary gland morphogenesis / limb bud formation / endochondral bone growth / reproductive structure development / embryonic digestive tract morphogenesis / membranous septum morphogenesis / positive regulation of epithelial cell proliferation involved in lung morphogenesis / lung lobe morphogenesis / organ growth / branching involved in prostate gland morphogenesis / mesenchymal cell differentiation / fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development / ventricular zone neuroblast division / positive regulation of phospholipase activity / FGFR2b ligand binding and activation / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / positive regulation of mesenchymal cell proliferation / Phospholipase C-mediated cascade; FGFR2 / embryonic cranial skeleton morphogenesis / regulation of osteoblast proliferation / fibroblast growth factor receptor activity / embryonic pattern specification / lung alveolus development / pyramidal neuron development / outflow tract septum morphogenesis / ureteric bud development / hair follicle morphogenesis / regulation of smoothened signaling pathway / mesodermal cell differentiation / digestive tract development / inner ear morphogenesis / bone morphogenesis / odontogenesis / skeletal system morphogenesis / midbrain development / Signaling by FGFR2 IIIa TM / prostate epithelial cord elongation / prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis / regulation of osteoblast differentiation / PI-3K cascade:FGFR2 / fibroblast growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / bone mineralization / positive regulation of cell division / cell fate commitment / fibroblast growth factor binding / negative regulation of keratinocyte proliferation / epithelial to mesenchymal transition / lung development / embryonic organ development / PI3K Cascade / post-embryonic development / cellular response to transforming growth factor beta stimulus / regulation of ERK1 and ERK2 cascade / positive regulation of cardiac muscle cell proliferation / positive regulation of Wnt signaling pathway / cellular response to retinoic acid / positive regulation of vascular associated smooth muscle cell proliferation / SHC-mediated cascade:FGFR2 / axonogenesis / FRS-mediated FGFR2 signaling / epithelial cell differentiation / Signaling by FGFR2 in disease / positive regulation of cell cycle / peptidyl-tyrosine phosphorylation / animal organ morphogenesis / positive regulation of epithelial cell proliferation / excitatory synapse / Negative regulation of FGFR2 signaling / bone development / receptor protein-tyrosine kinase / in utero embryonic development / Constitutive Signaling by Aberrant PI3K in Cancer
Similarity search - Function
Fibroblast growth factor receptor family / 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. ...Fibroblast growth factor receptor family / 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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
Fibroblast growth factor receptor 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsCeska, T.A. / Owens, R. / Doyle, C. / Hamlyn, P. / Crabbe, T. / Moffat, D. / Davis, J. / Martin, R. / Perry, M.J.
CitationJournal: To be Published
Title: The Fgfr2 Tyrosine Kinase Domain
Authors: Ceska, T.A. / Owens, R. / Doyle, C. / Hamlyn, P. / Crabbe, T. / Moffat, D. / Davis, J. / Martin, R. / Perry, M.J.
History
DepositionJul 31, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2893
Polymers36,0971
Non-polymers1922
Water2,810156
1
A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules

A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules

A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules

A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,15512
Polymers144,3864
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
crystal symmetry operation2_565-x,-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)69.758, 80.983, 120.059
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein FIBROBLAST GROWTH FACTOR RECEPTOR 2 / FGFR-2 / KERATINOCYTE


Mass: 36096.586 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN RESIDUES 465-768
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: P21802, EC: 2.7.1.112
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growpH: 5.9
Details: 32% AMMONIUM SULFATE, TRIS/MALEIC ACID BUFFER, PH 5.9

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 75710 / % possible obs: 98.6 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 10.8
Reflection shellHighest resolution: 2.4 Å / Rmerge(I) obs: 0.163 / % possible all: 97.1

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Processing

Software
NameVersionClassification
X-PLOR98refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FGK

1fgk


Resolution: 2.4→40 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1332 10 %RANDOM
Rwork0.214 ---
obs0.214 11986 98.6 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 10 156 2377
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.268
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.177
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO

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