5DNF: CC chemokine 5 (CCL5) oligomer

Crystal structure of CC chemokine 5 (CCL5) oligomer in complex with heparin. Determined by X-ray diffraction at 2.55 Å resolution. Released 13 Apr 2016.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 9
Atoms: 5,295
Mol. weight: 73.68 kDa
Ligands: BGC, GLA
Released: 13 Apr 2016

Explore 5DNF in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5DNF contains 36 α-helices and 43 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, D, F and H: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	8-10	3	2
α-helix	18-20	3
α-helix	21-23	3
β-strand	24-29	6	3
α-helix	30-31	2
β-strand	39-43	5	3
β-strand	48-51	4	3
α-helix	56-66	11

Chains B, E and G: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	6	1	3
β-strand	8-10	3	2
α-helix	18-20	3
α-helix	21-23	3
β-strand	24-29	6	1
α-helix	30-31	2
β-strand	39-43	5	1
β-strand	48-51	4	1
α-helix	56-66	11

Chain C: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	4
β-strand	8-10	3	5
α-helix	18-19	2
α-helix	21-23	3
β-strand	24-29	6	6
α-helix	30-31	2
β-strand	39-43	5	6
β-strand	48-51	4	6
α-helix	56-66	11

Chain I: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	18-20	3
α-helix	21-23	3
β-strand	24-29	6	13
α-helix	30-31	2
β-strand	39-43	5	13
β-strand	48-51	4	13
α-helix	56-66	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C motif chemokine 5	A, B, C, D, E, F, G, H, I	protein	65	Homo sapiens	P13501 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H, I), FASTA

>5DNF_1 C-C motif chemokine 5 (chains A, B, C, D, E, F, G, H, I)
SSDTTPCCFAYIARPLPRAHIKEYFYTSGKCSNPAVVFVTRKNRQVCANPEKKWVREYIN
SLEMS

Ligands and cofactors

ID	Name	Formula	Copies
BGC	beta-D-glucopyranose	C6 H12 O6	5
GLA	alpha-D-galactopyranose	C6 H12 O6	6

Water and common crystallization additives (TRS, CL, SO4) are not listed.

Primary citation

Structural basis for oligomerization and glycosaminoglycan binding of CCL5 and CCL3. Liang, W.G., Triandafillou, C.G., Huang, T.Y. et al. Proc Natl Acad Sci U S A (2016) 113:5000-5005. DOI 10.1073/pnas.1523981113 · PubMed

Other PDB entries of the same protein (UniProt P13501 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5COY 1.44 Å, Crystal structure of CC chemokine 5 (CCL5)
6STK 1.52 Å, Crystal structure of the CC-chemokine 5 (CCL5) E66S mutation
1B3A 1.6 Å, Total chemical synthesis and high-resolution crystal structure of the potent anti-HIV…
1EQT 1.6 Å, Met-rantes
6AEZ 1.63 Å, Crystal structure of human CCL5 trimer
1U4P 1.7 Å, Crystal Structure of human RANTES mutant K45E
2VXW 1.7 Å, Structural and Functional Studies of the Potent Anti-HIV Chemokine Variant P2-RANTES
1U4L 2.0 Å, human RANTES complexed to heparin-derived disaccharide I-S
1U4M 2.0 Å, human RANTES complexed to heparin-derived disaccharide III-S
1U4R 2.2 Å, Crystal Structure of human RANTES mutant 44-AANA-47
5UIW 2.2 Å, Crystal Structure of CC Chemokine Receptor 5 (CCR5) in complex with high potency HIV…
5L2U 2.28 Å, Oligomer crystal structure of CC chemokine 5 (CCL5)

Browse structure collections

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