SAXSdb — 5ltl

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

C-C motif chemokine 16

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 24–120 Chain B； UniProt 24–120	Not recorded	NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.05 M sodium phosphate, 0.5 M sodium chloride, 10 % (v/v) glycerol, 1.6 M sodium citrate	Resolution 1.45 Å R-free 0.198

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 5LTL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7SCT Crystal Structure of the Tick Evasin EVA-AAM1001 Complexed to Human Chemokine CCL16 Deposited 2021-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 23–120（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；1.26 M (NH4)2SO4 (Precipitant),0.1 M HEPES 7.5 pH (Buffer)	Resolution 1.84 Å R-free 0.210
8FK9 Crystal Structure of the Tick Evasin EVA-ACA1001 Complexed to Human Chemokine CCL16 Deposited 2022-12-21	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 23–120（98 aa） Chain D 23–120（98 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1 M HEPES 7 pH, 0.5 %v/v Jeff ED-2001, 1.1 M Na2 Malon	Resolution 2.70 Å R-free 0.266

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CCL16_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–100； UniProt 24–120 Author chain B； PDBConstruct 4–100； UniProt 24–120

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	5ltl
Deposition date deposition_date	2016-09-07
Structure title title	Structure of human chemokine CCL16
Keywords keywords	Chemokine, CC-type, Chemotaxis, 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	18.24 Å
Radius of gyration Rg (electron density) rg_electron	17.83 Å
Forward intensity I(0) i0	4310370.00
Molecular weight molecular_weight	15404.0 kDa
Excluded volume excluded_volume	19469 Å³
Envelope volume envelope_volume	23068 Å³
Hydration-shell volume shell_volume	11816 Å³
Envelope diameter envelope_diameter	58.7 Å
Shell Rg shell_rg	22.15 Å
Envelope Rg envelope_rg	17.89 Å
Shape Rg shape_rg	17.89 Å
Total Rg total_rg	18.43 Å
Total atoms total_atoms	1082
Residues n_residues	137
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	61.1 Å
Rg (real space) rg_real	18.37 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	4.3100e+06
I(0) uncertainty (real space) i0_real_error	5.6430e+04
Rg (reciprocal space) rg_reciprocal	18.35 Å
I(0) (reciprocal space) i0_reciprocal	4310000.0000
Solution quality estimate total_estimate	0.8356
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.3 Å
Skewness Skewness skewness	0.489
Kurtosis Kurtosis kurtosis	-0.424
Angular range angular_range	— – 0.4350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1397000.0000
Real-space data points n_real_points	75
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.686; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.829; Smooth: 0.976

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	C-C motif chemokine 16
Molecular weight formula_weight	11458.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1238

GPSQPKVPEWVNTPSTCCLKYYEKVLPRRLVVGYRKALNCHLPAIIFVTKRNREVCTNPNDDWVQEYIKDPNLPLLPTRNLSTVKIITAKNGQPQLLNSQ

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 K-12

Entity 2 Entity 2 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	90

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d5ltla_
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.9.1.0 — automated matches

Domain ID domain_id	d5ltlb_
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.9.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	5ltlA00
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	5ltlB00
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	136.350 Å
Unit-cell length b length_b	24.590 Å
Unit-cell length c length_c	37.970 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.12 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	37.910 Å
R factor r_factor	0.1719
R_work r_work	0.1705
R_free r_free	0.1976

fit	/app/data/saxs_computation/lt/5ltl/5ltl.fit
pddf	/app/data/pr_computation/lt/5ltl/5ltl.pr.out
profile	/app/data/saxs_computation/lt/5ltl/5ltl.dat

Structure of human chemokine CCL16

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

C-C motif chemokine 16

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