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- PDB-1oec: FGFr2 kinase domain -

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Basic information

Entry
Database: PDB / ID: 1oec
TitleFGFr2 kinase domain
ComponentsFIBROBLAST GROWTH FACTOR RECEPTOR 2
KeywordsTRANSFERASE / FGFR2 KINASE DOMAIN / RECEPTOR TYROSINE KINASE
Function / homology
Function and homology information


2 iron, 2 sulfur cluster binding / oxidoreductase activity / metal ion binding
Similarity search - Function
NADP-reducing hydrogenase subunit HndA / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Thioredoxin-like [2Fe-2S] ferredoxin / Thioredoxin-like superfamily / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 ...NADP-reducing hydrogenase subunit HndA / Respiratory-chain NADH dehydrogenase 24 Kd subunit signature. / NuoE domain / NADH-quinone oxidoreductase subunit E-like / NADH-quinone oxidoreductase subunit E, N-terminal / Thioredoxin-like [2Fe-2S] ferredoxin / Thioredoxin-like superfamily / Protein tyrosine and serine/threonine kinase / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
4-ARYL-2-PHENYLAMINO PYRIMIDINE / NADH-quinone oxidoreductase, E subunit
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 Crystal Structure of the Fgfr2 Tyrosine Kinase Domain in Complex with 4-Aryl-2-Phenylamino Pyrimidine Angiogenesis Inhibitors
Authors: Ceska, T.A. / Owens, R. / Doyle, C. / Hamlyn, P. / Crabbe, T. / Moffat, D. / Davis, J. / Martin, R. / Perry, M.J.
History
DepositionMar 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2004Provider: 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

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Assembly

Deposited unit
A: FIBROBLAST GROWTH FACTOR RECEPTOR 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7414
Polymers36,0971
Non-polymers6443
Water2,900161
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)146,96316
Polymers144,3864
Non-polymers2,57612
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)69.760, 80.500, 120.170
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 GROWTH FACTOR RECEPTOR 2


Mass: 36096.586 Da / Num. of mol.: 1 / Fragment: TYROSINE KINASE DOMAIN, RESIDUES 456-768
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: Chemical ChemComp-AA2 / 4-ARYL-2-PHENYLAMINO PYRIMIDINE / 4-[4-(1-AMINO-1-METHYLETHYL)PHENYL]-5-CHLORO-N-[4-(2-MORPHOLIN-4-YLETHYL)PHENYL]PYRIMIDIN-2-AMINE


Mass: 451.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C25H30ClN5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRECEPTOR FOR ACIDIC AND BASIC FIBROBLAST GROWTH FACTORS.

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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: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal growpH: 5.9 / Details: pH 5.90

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 87022 / % possible obs: 98 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 22.1
Reflection shellResolution: 2.4→2.45 Å / Rmerge(I) obs: 0.199 / % possible all: 78.9

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GJO

1gjo


Resolution: 2.4→100 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
Details: THERE ARE TWO DISORDERED REGIONS. 504-506 AND 581-595 IN ADDITION DISORDERED ATOMS OF RESIDUES C491 AND F492 HAVE BEEN OMITTED.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1373 10 %RANDOM
Rwork0.211 ---
obs0.211 13496 98 %-
Displacement parametersBiso mean: 37.5 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 42 161 2414
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_deg1.24
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_d1.136
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 file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPH19.PEP
X-RAY DIFFRACTION2AA2.PARAA2.TOP

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