SAXSdb — 2p39

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

Fibroblast growth factor 23

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 25–179	Not recorded	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；100 mM Tris-HCl, 1.0 M (NH4)2SO4, 10 mM [Co(NH3)6]Cl3, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.214

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.

Other PDB	Difference from Current Entry 2P39	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5W21 Crystal Structure of a 1:1:1 FGF23-FGFR1c-aKlotho Ternary Complex Deposited 2017-06-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 25–204（180 aa） Fragment：UNP residues 25-204	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 7 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；22% PEG350 MME, 0.1 M Tris-HCl, pH 8.0, 1 mM reduced glutathione, 1 mM oxidized glutathione	Resolution 3.00 Å R-free 0.278
6S22 Crystal structure of the TgGalNAc-T3 in complex with UDP, manganese and FGF23c Deposited 2019-06-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 170–181（12 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 14 SO4 SULFATE ION × 1 UDP URIDINE-5'-DIPHOSPHATE × 1 MN MANGANESE (II) ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1 NGA 2-acetamido-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；Morpheus precipitant mix 4, nitrate phosphate buffer and Morpheus buffer System 1	Resolution 1.96 Å R-free 0.216
7YSH Cryo-EM Structure of FGF23-FGFR1c-aKlotho-HS Quaternary Complex Deposited 2022-08-12	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–251（227 aa）	Not recorded	ZN ZINC ION × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.74 Å
7YSU Cryo-EM Structure of FGF23-FGFR3c-aKlotho-HS Quaternary Complex Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–203（179 aa）	Not recorded	ZN ZINC ION × 1 CU COPPER (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
7YSW Cryo-EM Structure of FGF23-FGFR4-aKlotho-HS Quaternary Complex Deposited 2022-08-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 25–203（179 aa）	Not recorded	CU COPPER (II) ION × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	FGF23_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–155； UniProt 25–179

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2p39
Deposition date deposition_date	2007-03-08
Structure title title	Crystal structure of human FGF23
Keywords keywords	atypical beta-trefoil fold, SIGNALING PROTEIN; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	16.10 Å
Radius of gyration Rg (electron density) rg_electron	14.94 Å
Forward intensity I(0) i0	6013080.00
Molecular weight molecular_weight	16701.0 kDa
Excluded volume excluded_volume	20388 Å³
Envelope volume envelope_volume	23362 Å³
Hydration-shell volume shell_volume	13338 Å³
Envelope diameter envelope_diameter	52.2 Å
Shell Rg shell_rg	20.69 Å
Envelope Rg envelope_rg	15.34 Å
Shape Rg shape_rg	14.88 Å
Total Rg total_rg	16.13 Å
Total atoms total_atoms	1168
Residues n_residues	142
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	52.5 Å
Rg (real space) rg_real	15.99 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	6.0130e+06
I(0) uncertainty (real space) i0_real_error	6.3420e+04
Rg (reciprocal space) rg_reciprocal	16.00 Å
I(0) (reciprocal space) i0_reciprocal	6013000.0000
Solution quality estimate total_estimate	0.8088
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.2 Å
Skewness Skewness skewness	0.120
Kurtosis Kurtosis kurtosis	-0.378
Angular range angular_range	— – 0.4950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	813300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Fibroblast growth factor 23
Molecular weight formula_weight	17856.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1261

YPNASPLLGSSWGGLIHLYTATARNSYHLQIHKNGHVDGAPHQTIYSALMIRSEDAGFVVITGVMSRRYLCMDFRGNIFGSHYFDPENCRFQHQTLENGYDVYHSPQYHFLVSLGRAKRAFLPGMNPPPYSQFLSRRNEIPLIHFNTPIPRRHTR

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	1,3,4,6-tetra-O-sulfo-beta-D-fructofuranose-(2-1)-2,3,4,6-tetra-O-sulfonato-alpha-D-glucopyranose
Molecular weight formula_weight	982.8 kDa
Source method src_method	man
Copy count entity_count	1

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2p39a_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.1 — Cytokine
Family Family family	b.42.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2p39A00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	38.811 Å
Unit-cell length b length_b	47.094 Å
Unit-cell length c length_c	84.931 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	25.000 Å
R factor r_factor	—
R_work r_work	0.2030
R_free r_free	0.2140

fit	/app/data/saxs_computation/p3/2p39/2p39.fit
pddf	/app/data/pr_computation/p3/2p39/2p39.pr.out
profile	/app/data/saxs_computation/p3/2p39/2p39.dat

Crystal structure of human FGF23

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

Fibroblast growth factor 23

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction