SAXSdb — 5eki

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

C-C motif chemokine 21

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
2	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
3	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	water × 1	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	SULFATE ION × 1 water × 1	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 6	SULFATE ION × 5 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCL21_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–79； UniProt 24–102 Author chain B； PDBConstruct 1–79； UniProt 24–102 Author chain C； PDBConstruct 1–79； UniProt 24–102 Author chain D； PDBConstruct 1–79； UniProt 24–102 Author chain E； PDBConstruct 1–79； UniProt 24–102 Author chain F； PDBConstruct 1–79； UniProt 24–102

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	5eki
Deposition date deposition_date	2015-11-03
Structure title title	Crystal Structure of Truncated CCL21
Keywords keywords	Cytokine, Chemokine, Chemotaxis, Inflammation, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

5eki__assembly_7__model_1

Assembly 7 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5eki__assembly_7__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5eki__assembly_7__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	25.77 Å
Rg (electron density)	25.33 Å
Total Rg	26.10 Å
Atom count	3452
Residues	427
Excluded volume	62121 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5eki__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5eki__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5eki__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`5eki__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`5eki__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`5eki__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`5eki__assembly_7__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	C-C motif chemokine 21
Molecular weight formula_weight	8864.3 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3639

SDGGAQDCCLKYSQRKIPAKVVRSYRKQEPSLGCSIPAILFLPRKRSQAELCADPKELWVQQLMQHLDKTPSPQKPAQG

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d5ekia_
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	d5ekib_
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	d5ekic_
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	d5ekid_
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	d5ekie_
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	d5ekif_
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 (6 domains)

Domain ID domain_id	5ekiA00
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	5ekiB00
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	5ekiC00
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	5ekiD00
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	5ekiE00
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	5ekiF00
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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Unit-cell length a length_a	65.752 Å
Unit-cell length b length_b	58.244 Å
Unit-cell length c length_c	66.054 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.94 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	57.240 Å
R factor r_factor	0.2127
R_work r_work	0.2102
R_free r_free	0.2622

Crystal Structure of Truncated CCL21

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

C-C motif chemokine 21

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5eki__assembly_7__model_1

5eki__assembly_7__model_1 | I(q)

5eki__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal Structure of Truncated CCL21

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

C-C motif chemokine 21

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

5eki__assembly_7__model_1

5eki__assembly_7__model_1 | I(q)

5eki__assembly_7__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)