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- PDB-3grw: FGFR3 in complex with a Fab -

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Basic information

Entry
Database: PDB / ID: 3grw
TitleFGFR3 in complex with a Fab
Components
  • Fab heavy chain
  • Fab light chain
  • Fibroblast growth factor receptor 3
KeywordsTRANSFERASE/IMMUNE SYSTEM / FGFR3 / Fab / protein-protein complex / receptor tyrosine kinase / ATP-binding / Immunoglobulin domain / Kinase / Membrane / Nucleotide-binding / Receptor / Transferase / Transmembrane / Tyrosine-protein kinase / TRANSFERASE-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


fibroblast growth factor receptor activity / fibroblast growth factor binding / receptor protein-tyrosine kinase / positive regulation of MAPK cascade / receptor complex / positive regulation of cell population proliferation / ATP binding / plasma membrane
Similarity search - Function
Fibroblast growth factor receptor 3 transmembrane domain / Fibroblast growth factor receptor family / 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 3 transmembrane domain / Fibroblast growth factor receptor family / 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 / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWiesmann, C.
CitationJournal: J.Clin.Invest. / Year: 2009
Title: Antibody-based targeting of FGFR3 in bladder carcinoma and t(4;14)-positive multiple myeloma in mice.
Authors: Qing, J. / Du, X. / Chen, Y. / Chan, P. / Li, H. / Wu, P. / Marsters, S. / Stawicki, S. / Tien, J. / Totpal, K. / Ross, S. / Stinson, S. / Dornan, D. / French, D. / Wang, Q.R. / Stephan, J.P. ...Authors: Qing, J. / Du, X. / Chen, Y. / Chan, P. / Li, H. / Wu, P. / Marsters, S. / Stawicki, S. / Tien, J. / Totpal, K. / Ross, S. / Stinson, S. / Dornan, D. / French, D. / Wang, Q.R. / Stephan, J.P. / Wu, Y. / Wiesmann, C. / Ashkenazi, A.
History
DepositionMar 26, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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 3
L: Fab light chain
H: Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4365
Polymers75,1193
Non-polymers3172
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7190 Å2
ΔGint-38 kcal/mol
Surface area30440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.049, 99.329, 143.657
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules LH

#2: Antibody Fab light chain


Mass: 23287.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)
#3: Antibody Fab heavy chain


Mass: 24992.848 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Protein selected by phage display / Production host: Escherichia coli (E. coli)

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Fibroblast growth factor receptor 3


Mass: 26838.121 Da / Num. of mol.: 1 / Fragment: domains 2 and 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NI16
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 275 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.76 Å3/Da / Density % sol: 55.38 %
Crystal growTemperature: 277 K / Method: evaporation / pH: 6.5
Details: 40% MPD, 5% PEG 8000, 0.1M Sodium Cacodylate, pH 6.5, EVAPORATION, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2007 / Details: Mirror
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→25 Å / Num. all: 49851 / Num. obs: 49786 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 10.29 / SU ML: 0.123 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.184 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22846 2499 5.1 %RANDOM
Rwork0.18933 ---
obs0.19134 46714 99.94 %-
all-46744 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.486 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2---0.41 Å20 Å2
3---2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4981 0 19 274 5274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225127
X-RAY DIFFRACTIONr_bond_other_d0.0070.023442
X-RAY DIFFRACTIONr_angle_refined_deg1.4321.9566986
X-RAY DIFFRACTIONr_angle_other_deg0.9213.0038383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7955647
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08523.768207
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76615811
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6321528
X-RAY DIFFRACTIONr_chiral_restr0.0860.2783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025709
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021027
X-RAY DIFFRACTIONr_nbd_refined0.1860.2718
X-RAY DIFFRACTIONr_nbd_other0.2060.23250
X-RAY DIFFRACTIONr_nbtor_refined0.170.22318
X-RAY DIFFRACTIONr_nbtor_other0.0840.22829
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1830.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.3062.54141
X-RAY DIFFRACTIONr_mcbond_other0.6332.51310
X-RAY DIFFRACTIONr_mcangle_it4.75255244
X-RAY DIFFRACTIONr_scbond_it4.1062.52251
X-RAY DIFFRACTIONr_scangle_it5.37851742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.143 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.336 132 -
Rwork0.243 2715 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 28.8768 Å / Origin y: 2.9451 Å / Origin z: -26.265 Å
111213212223313233
T-0.0303 Å20.0189 Å20.0329 Å2--0.0295 Å20.0075 Å2---0.0179 Å2
L0.51 °20.2441 °2-0.0799 °2-0.2455 °20.0152 °2--0.0789 °2
S0.0267 Å °-0.0301 Å °-0.0226 Å °0.0277 Å °-0.0064 Å °-0.0028 Å °0.0126 Å °0.0148 Å °-0.0203 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L215 - 311
2X-RAY DIFFRACTION1H223 - 339
3X-RAY DIFFRACTION1A2 - 410
4X-RAY DIFFRACTION1H222
5X-RAY DIFFRACTION1A1
6X-RAY DIFFRACTION1L1 - 214
7X-RAY DIFFRACTION1H1 - 216
8X-RAY DIFFRACTION1A150 - 355

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