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- PDB-1afc: STRUCTURAL STUDIES OF THE BINDING OF THE ANTI-ULCER DRUG SUCROSE ... -

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Basic information

Entry
Database: PDB / ID: 1afc
TitleSTRUCTURAL STUDIES OF THE BINDING OF THE ANTI-ULCER DRUG SUCROSE OCTASULFATE TO ACIDIC FIBROBLAST GROWTH FACTOR
ComponentsACIDIC FIBROBLAST GROWTH FACTOR
KeywordsGROWTH FACTOR
Function / homology
Function and homology information


FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR1c ligand binding and activation / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR3 ...FGFR4 ligand binding and activation / FGFR1b ligand binding and activation / FGFR3b ligand binding and activation / FGFR3c ligand binding and activation / FGFR1c ligand binding and activation / FGFR2c ligand binding and activation / FGFR2b ligand binding and activation / Phospholipase C-mediated cascade: FGFR1 / Phospholipase C-mediated cascade; FGFR2 / Phospholipase C-mediated cascade; FGFR3 / Phospholipase C-mediated cascade; FGFR4 / Downstream signaling of activated FGFR1 / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR1 signaling / SHC-mediated cascade:FGFR2 / FRS-mediated FGFR2 signaling / SHC-mediated cascade:FGFR3 / FRS-mediated FGFR3 signaling / FRS-mediated FGFR4 signaling / SHC-mediated cascade:FGFR4 / PI-3K cascade:FGFR1 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR4 / PI3K Cascade / PIP3 activates AKT signaling / RAF/MAP kinase cascade / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / Negative regulation of FGFR1 signaling / Negative regulation of FGFR2 signaling / Negative regulation of FGFR3 signaling / Negative regulation of FGFR4 signaling / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / regulation of endothelial cell chemotaxis to fibroblast growth factor / fibroblast growth factor receptor binding / organ induction / S100 protein binding / positive regulation of sprouting angiogenesis / positive regulation of intracellular signal transduction / positive regulation of cell division / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / neurogenesis / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / growth factor activity / wound healing / positive regulation of cholesterol biosynthetic process / integrin binding / positive regulation of angiogenesis / heparin binding / cellular response to heat / cell cortex / angiogenesis / positive regulation of ERK1 and ERK2 cascade / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / 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
sucrose octasulfate / Fibroblast growth factor 1
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsZhu, X. / Hsu, B.T. / Rees, D.C.
Citation
Journal: Structure / Year: 1993
Title: Structural studies of the binding of the anti-ulcer drug sucrose octasulfate to acidic fibroblast growth factor.
Authors: Zhu, X. / Hsu, B.T. / Rees, D.C.
#1: Journal: Science / Year: 1991
Title: Three-Dimensional Structures of Acidic and Basic Fibroblast Growth Factors
Authors: Zhu, X. / Komiya, H. / Chirino, A. / Faham, S. / Fox, G.M. / Arakawa, T. / Hsu, B.T. / Rees, D.C.
History
DepositionJul 13, 1993Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: ACIDIC FIBROBLAST GROWTH FACTOR
B: ACIDIC FIBROBLAST GROWTH FACTOR
C: ACIDIC FIBROBLAST GROWTH FACTOR
D: ACIDIC FIBROBLAST GROWTH FACTOR
E: ACIDIC FIBROBLAST GROWTH FACTOR
F: ACIDIC FIBROBLAST GROWTH FACTOR
G: ACIDIC FIBROBLAST GROWTH FACTOR
H: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,83016
Polymers126,9688
Non-polymers7,8628
Water00
1
A: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: ACIDIC FIBROBLAST GROWTH FACTOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8542
Polymers15,8711
Non-polymers9831
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.600, 110.600, 172.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
ACIDIC FIBROBLAST GROWTH FACTOR


Mass: 15871.007 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P03968
#2: Polysaccharide
1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose / sucrose octasulfate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 982.803 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose octasulfate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5_1*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O][a2122h-1a_1-5_2*OSO/3=O/3=O_3*OSO/3=O/3=O_4*OSO/3=O/3=O_6*OSO/3=O/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf1SO33SO34SO36SO3]{[(2+1)][a-D-Glcp2SO33SO34SO36SO3]{}}LINUCSPDB-CARE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal grow
*PLUS
pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein solution1drop
20.1 M1reservoirMgCl2
327.5 %PEG80001reservoir
40.1 MN-2-acetamidoiminodiacetic1reservoir
53.3 mMSOS1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. obs: 31326 / % possible obs: 95 % / Num. measured all: 138212 / Rmerge(I) obs: 0.118

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.204 / Rfactor obs: 0.204 / Highest resolution: 2.7 Å
Refinement stepCycle: LAST / Highest resolution: 2.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7872 0 440 0 8312
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
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_deg2.7
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_d
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
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor obs: 0.204
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.7

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