SAXSdb — 1f2l

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

FRACTALKINE

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	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 25–100 Chain B； UniProt 25–100 Chain C； UniProt 25–100 Chain D； UniProt 25–100	Fragment：CHEMOKINE DOMAIN	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5；298 K；sodium formate, disodium citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.321

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 1F2L	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1B2T SOLUTION STRUCTURE OF THE CX3C CHEMOKINE DOMAIN OF FRACTALKINE Deposited 1998-12-01	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 25–100（76 aa） Fragment：CHEMOKINE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；295.5 K；Pressure 1	Resolution not provided
4XT1 Structure of a nanobody-bound viral GPCR bound to human chemokine CX3CL1 Deposited 2015-01-22	Different construct Different mutation/modification 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 25–101（77 aa） Fragment：UNP residues 25-101	Mutation：N9A Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 2 OLC (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate × 6 UNL UNKNOWN LIGAND × 7 SIN SUCCINIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 6.3；293 K；PEG 300, MES, sodium succinate, polypropylene glycol 400	Resolution 2.89 Å R-free 0.249
4XT3 Structure of a viral GPCR bound to human chemokine CX3CL1 Deposited 2015-01-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	UNL UNKNOWN LIGAND × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIPIDIC CUBIC PHASE；pH 7.4；293 K；PEG 300, HEPES, ammonium phosphate	Resolution 3.80 Å R-free 0.322
7RKF Structure of CX3CL1-US28-G11iN18-scFv16 in TL-state Deposited 2021-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	GDP GUANOSINE-5'-DIPHOSPHATE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 4.00 Å
7RKM Structure of CX3CL1-US28-Gi-scFv16 in C-state Deposited 2021-07-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.50 Å
7RKN Structure of CX3CL1-US28-Gi-scFv16 in OC-state Deposited 2021-07-22	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain L 25–101（77 aa） Fragment：UNP residues 25-101	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE；1 s blotting before plunging	Resolution 3.60 Å
7XBX Cryo-EM structure of the human chemokine receptor CX3CR1 in complex with CX3CL1 and Gi1 Deposited 2022-03-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 25–100（76 aa）	Mutation：G35C,I222L,L278C,C323S,M352V Non-standard monomer：Yes (specific site not provided by mmCIF)	CLR CHOLESTEROL × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	X3CL1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–76； UniProt 25–100 Author chain B； PDBConstruct 1–76； UniProt 25–100 Author chain C； PDBConstruct 1–76； UniProt 25–100 Author chain D； PDBConstruct 1–76； UniProt 25–100

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	1f2l
Deposition date deposition_date	2000-05-26
Structure title title	CRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE
Keywords keywords	CHEMOATTRACTANT, Fractalkine, neurotactin, CYTOKINE; CYTOKINE
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	21.01 Å
Radius of gyration Rg (electron density) rg_electron	20.19 Å
Forward intensity I(0) i0	17040400.00
Molecular weight molecular_weight	30236.0 kDa
Excluded volume excluded_volume	37591 Å³
Envelope volume envelope_volume	46607 Å³
Hydration-shell volume shell_volume	19549 Å³
Envelope diameter envelope_diameter	68.0 Å
Shell Rg shell_rg	25.97 Å
Envelope Rg envelope_rg	19.99 Å
Shape Rg shape_rg	20.11 Å
Total Rg total_rg	21.19 Å
Total atoms total_atoms	2105
Residues n_residues	262
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	65.7 Å
Rg (real space) rg_real	20.92 Å
Rg uncertainty (real space) rg_real_error	0.30 Å
I(0) (real space) i0_real	1.7040e+07
I(0) uncertainty (real space) i0_real_error	2.1940e+05
Rg (reciprocal space) rg_reciprocal	20.94 Å
I(0) (reciprocal space) i0_reciprocal	17040000.0000
Solution quality estimate total_estimate	0.9100
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	23.8 Å
Skewness Skewness skewness	0.163
Kurtosis Kurtosis kurtosis	-0.576
Angular range angular_range	— – 0.3800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2801000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.947; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1f2la_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1f2lb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1f2lc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

Domain ID domain_id	d1f2ld_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.9 — IL8-like
Superfamily Superfamily superfamily	d.9.1 — Interleukin 8-like chemokines
Family Family family	d.9.1.1 — Interleukin 8-like chemokines

CATH v4.4 (4 domains)

Domain ID domain_id	1f2lA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1f2lB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1f2lC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	1f2lD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Unit-cell length a length_a	110.473 Å
Unit-cell length b length_b	110.473 Å
Unit-cell length c length_c	123.994 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	48

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	15.000 Å
R factor r_factor	0.2375
R_work r_work	0.2377
R_free r_free	0.3212

Description description	FRACTALKINE
Molecular weight formula_weight	8656.0 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	2369

CRYSTAL STRUCTURE OF CHEMOKINE DOMAIN OF FRACTALKINE

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

FRACTALKINE

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	264

fit	/app/data/saxs_computation/f2/1f2l/1f2l.fit
pddf	/app/data/pr_computation/f2/1f2l/1f2l.pr.out
profile	/app/data/saxs_computation/f2/1f2l/1f2l.dat