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- PDB-3k1x: Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate -

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Basic information

Entry
Database: PDB / ID: 3k1x
TitleAcidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate
ComponentsHeparin-binding growth factor 1
KeywordsHORMONE / acidic fibroblast growth factor / inhibitors / ACETYLATION
Function / homology
Function and homology information


mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process ...mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / positive regulation of cholesterol biosynthetic process / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / 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 hepatocyte proliferation / S100 protein binding / positive regulation of intracellular signal transduction / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / positive regulation of sprouting angiogenesis / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of cell division / PI3K Cascade / fibroblast growth factor receptor signaling pathway / anatomical structure morphogenesis / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / Hsp70 protein binding / Signaling by FGFR1 in disease / activation of protein kinase B activity / positive regulation of endothelial cell migration / extracellular matrix / epithelial cell proliferation / positive regulation of epithelial cell proliferation / Negative regulation of FGFR3 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / animal organ morphogenesis / Negative regulation of FGFR1 signaling / growth factor activity / positive regulation of MAP kinase activity / lung development / wound healing / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / integrin binding / PIP3 activates AKT signaling / heparin binding / cellular response to heat / cell cortex / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / angiogenesis / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of cell migration / positive regulation of cell population proliferation / positive regulation of gene expression / signal transduction / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Mainly Beta
Similarity search - Domain/homology
2,5-dihydroxybenzenesulfonic acid / Fibroblast growth factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsRomero, A. / Fernandez, I.S. / Gimenez-Gallego, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Gentisic acid, a compound associated with plant defense and a metabolite of aspirin, heads a new class of in vivo fibroblast growth factor inhibitors.
Authors: Fernandez, I.S. / Cuevas, P. / Angulo, J. / Lopez-Navajas, P. / Canales-Mayordomo, A. / Gonzalez-Corrochano, R. / Lozano, R.M. / Valverde, S. / Jimenez-Barbero, J. / Romero, A. / Gimenez-Gallego, G.
History
DepositionSep 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Heparin-binding growth factor 1
B: Heparin-binding growth factor 1
C: Heparin-binding growth factor 1
D: Heparin-binding growth factor 1
E: Heparin-binding growth factor 1
F: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8978
Polymers88,5166
Non-polymers3802
Water2,774154
1
A: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9432
Polymers14,7531
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Heparin-binding growth factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,9432
Polymers14,7531
Non-polymers1901
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Heparin-binding growth factor 1


Theoretical massNumber of molelcules
Total (without water)14,7531
Polymers14,7531
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.022, 47.349, 97.975
Angle α, β, γ (deg.)90.00, 106.64, 90.00
Int Tables number3
Space group name H-MP121

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Components

#1: Protein
Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / aFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 14752.703 Da / Num. of mol.: 6 / Fragment: Heparin-binding, UNP residues 24-153
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pRAT / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#2: Chemical ChemComp-DBX / 2,5-dihydroxybenzenesulfonic acid


Mass: 190.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.44 Å3/Da / Density % sol: 49.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0. ...Details: Crystals of thecomplex between FGF-1 and 2,5-DHPS (2,5-dihydroxyphenylsulfonate) were grown using the sitting drop vapour method at 295 K. Equal volumes of protein and inhibitor solutions, 0.75 and 1.5mM, respectively were mixed with drops containing 60% sodium/potassium tartrate buffered with 5mM sodium phosphate [pH 7.8]. The drops were equilibrated against 0.2ml of 1.3M Li2SO4 and typical crystals grew within two weeks with approximate dimensions of 0.7 x 0.5 x 0.2 mm. , VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 7, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.98→94.07 Å / Num. all: 59910 / Num. obs: 59016 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 29.604 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 16
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.342 / Mean I/σ(I) obs: 4.5 / Num. unique all: 8011 / % possible all: 92.8

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Processing

Software
NameVersionClassification
DNAdata collection
AMoREphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AXM

1axm


Resolution: 1.98→24.48 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / SU B: 5.774 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.28958 2981 5.1 %RANDOM
Rwork0.22718 ---
all0.232 59016 --
obs0.23041 56030 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.077 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20 Å20.61 Å2
2--1.01 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 1.98→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6228 0 24 154 6406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0226390
X-RAY DIFFRACTIONr_angle_refined_deg2.2731.9778622
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2455774
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35324.2300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.798151146
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.251536
X-RAY DIFFRACTIONr_chiral_restr0.1610.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.024854
X-RAY DIFFRACTIONr_nbd_refined0.2320.22576
X-RAY DIFFRACTIONr_nbtor_refined0.3170.24111
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2348
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2650.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.211
X-RAY DIFFRACTIONr_mcbond_it1.6691.53999
X-RAY DIFFRACTIONr_mcangle_it2.71326210
X-RAY DIFFRACTIONr_scbond_it3.59632753
X-RAY DIFFRACTIONr_scangle_it5.074.52412
LS refinement shellResolution: 1.981→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.409 204 -
Rwork0.299 3566 -
obs--86.61 %

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