5dnf

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

Method: X-RAY DIFFRACTION

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

C-C motif chemokine 5

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 9 其他Polymer 3	;2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ; × 3 alpha-D-galactopyranose × 6 beta-D-glucopyranose × 5 SULFATE ION × 5 CHLORIDE ION × 20 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 9	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCL5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–65； UniProt 27–91 Author chain B； PDBConstruct 1–65； UniProt 27–91 Author chain C； PDBConstruct 1–65； UniProt 27–91 Author chain D； PDBConstruct 1–65； UniProt 27–91 Author chain E； PDBConstruct 1–65； UniProt 27–91 Author chain F； PDBConstruct 1–65； UniProt 27–91 Author chain G； PDBConstruct 1–65； UniProt 27–91 Author chain H； PDBConstruct 1–65； UniProt 27–91 Author chain I； PDBConstruct 1–65； UniProt 27–91

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	5dnf
Deposition date deposition_date	2015-09-10
Structure title title	Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin
Keywords keywords	CC chemokine, high oligomer, CYTOKINE; CYTOKINE
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.

5dnf__assembly_1__model_1

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

Download this curve (.dat)

5dnf__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5dnf__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.81 Å
Rg (electron density)	33.61 Å
Total Rg	33.99 Å
Atom count	5066
Residues	585
Excluded volume	89822 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5dnf__assembly_1__model_1`	nonameric （9）	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 (8)

Entity 1 Entity 1 polymer

Description description	C-C motif chemokine 5
Molecular weight formula_weight	7514.6 kDa
Mutation mutation	S4TNR
Source method src_method	man
Copy count entity_count	9

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I
Atom count atom_count	5295

SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYINSLEMS

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 branched

Description description	;2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose ;
Molecular weight formula_weight	916.8 kDa
Source method src_method	man
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	alpha-D-galactopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	beta-D-glucopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	20

Entity 7 Entity 7 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	man
Copy count entity_count	1

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	210

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d5dnfa_
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	d5dnfb_
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	d5dnfc_
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	d5dnfd_
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	d5dnfe_
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	d5dnff_
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	d5dnfg_
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	d5dnfh_
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	d5dnfi_
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 (9 domains)

Domain ID domain_id	5dnfA00
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	5dnfB00
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	5dnfC00
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	5dnfD00
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	5dnfE00
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	5dnfF00
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	5dnfG00
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	5dnfH00
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	5dnfI00
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	121.190 Å
Unit-cell length b length_b	210.063 Å
Unit-cell length c length_c	123.827 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	72

Space group space_group	C 2 2 2
Space-group number int_tables_number	21
Crystal system crystal_system	—

Resolution resolution	2.549 Å
Low-resolution limit resolution_low	39.695 Å
R factor r_factor	0.1826
R_work r_work	0.1805
R_free r_free	0.2337

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

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

C-C motif chemokine 5

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

5dnf__assembly_1__model_1

5dnf__assembly_1__model_1 | I(q)

5dnf__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin

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

C-C motif chemokine 5

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

5dnf__assembly_1__model_1

5dnf__assembly_1__model_1 | I(q)

5dnf__assembly_1__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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (9 domains)

CATH v4.4 (9 domains)

7. Citations (1)