3k1x

Acidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate

Method: X-RAY DIFFRACTION Dmax: 121.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

Heparin-binding growth factor 1

Homo sapiens

UniProt P05230

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 DBX 2,5-dihydroxybenzenesulfonic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 DBX 2,5-dihydroxybenzenesulfonic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain C; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290
4 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain D; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290
5 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain E; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290
6 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain F; UniProt 24–153 Fragment:Heparin-binding, UNP residues 24-153 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.8;295 K;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 Resolution 1.98 Å R-free 0.290

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

96 other PDB entries and 212 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–130; UniProt 24–153 Author chain B; PDBConstruct 1–130; UniProt 24–153 Author chain C; PDBConstruct 1–130; UniProt 24–153 Author chain D; PDBConstruct 1–130; UniProt 24–153 Author chain E; PDBConstruct 1–130; UniProt 24–153 Author chain F; PDBConstruct 1–130; UniProt 24–153

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3k1x

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3k1x
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3k1x
Deposition date deposition_date2009-09-29
Structure title titleAcidic Fibroblast Growth Factor (FGF-1) complexed with dobesilate
Keywords keywordsacidic fibroblast growth factor, inhibitors, ACETYLATION, HORMONE; HORMONE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.41
Radius of gyration Rg (electron density) rg_electron37.37
Forward intensity I(0) i0123564000.00
Molecular weight molecular_weight88777.0 kDa
Excluded volume excluded_volume110790 ų
Envelope volume envelope_volume146040 ų
Hydration-shell volume shell_volume34738 ų
Envelope diameter envelope_diameter120.1
Shell Rg shell_rg40.67
Envelope Rg envelope_rg36.73
Shape Rg shape_rg37.37
Total Rg total_rg37.61
Total atoms total_atoms6252
Residues n_residues780
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.6
Rg (real space) rg_real37.67
Rg uncertainty (real space) rg_real_error1.09
I(0) (real space) i0_real1.2360e+08
I(0) uncertainty (real space) i0_real_error2.1830e+06
Rg (reciprocal space) rg_reciprocal37.52
I(0) (reciprocal space) i0_reciprocal123500000.0000
Solution quality estimate total_estimate0.8412
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7
Skewness Skewness skewness0.347
Kurtosis Kurtosis kurtosis-0.815
Angular range angular_range— – 0.2100 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9015000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.792; Smooth: 0.818

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3k1xa_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3k1xb_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3k1xc_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3k1xd_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3k1xe_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)
Domain ID domain_idd3k1xf_
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.1 — Cytokine
Family Family familyb.42.1.1 — Fibroblast growth factors (FGF)

CATH v4.4 (6 domains)

Domain ID domain_id3k1xA00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3k1xB00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3k1xC00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3k1xD00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3k1xE00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50
Domain ID domain_id3k1xF00
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50

8. Citations (1)

9. Files and Curves (10)