5D65: C-C motif chemokine 3

X-ray structure of macrophage inflammatory protein-1 alpha (CCL3) with heparin complex. Determined by X-ray diffraction at 3.1 Å resolution. Released 20 Apr 2016.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 2,855
Mol. weight: 42.03 kDa
Ligands: GLC, BGC
Released: 20 Apr 2016

Explore 5D65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5D65 contains 20 α-helices and 20 β-strands across 5 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.

Chain A: 5 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	1
α-helix	8-10	3
α-helix	19-21	3
α-helix	22-24	3
β-strand	25-30	6	2
α-helix	31-32	2
β-strand	40-44	5	2
β-strand	49-52	4	2
α-helix	57-67	11

Chains B and C: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	1
α-helix	19-21	3
α-helix	22-24	3
β-strand	25-30	6	3
α-helix	31-32	2
β-strand	40-44	5	3
β-strand	49-52	4	3
α-helix	57-67	11

Chain D: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	5
α-helix	19-20	2
α-helix	22-24	3
β-strand	25-30	6	6
α-helix	31-32	2
β-strand	40-44	5	6
β-strand	49-52	4	6
α-helix	57-67	11

Chain E: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	9-11	3	5
α-helix	19-21	3
α-helix	22-24	3
β-strand	25-30	6	7
β-strand	40-44	5	7
β-strand	49-52	4	7
α-helix	58-67	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-C motif chemokine 3	A, B, C, D, E	protein	70	Homo sapiens	P10147 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E), FASTA

>5D65_1 C-C motif chemokine 3 (chains A, B, C, D, E)
ASLAADTPTACCFSYTSRQIPQNFIADYFETSSQCSKPGVIFLTKRSRQVCADPSEEWVQ
KYVSDLELSA

Ligands and cofactors

ID	Name	Formula	Copies
GLC	alpha-D-glucopyranose	C6 H12 O6	1
BGC	beta-D-glucopyranose	C6 H12 O6	9

Water and common crystallization additives (CL) 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 P10147 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3FPU 1.76 Å, The crystallographic structure of the Complex between Evasin-1 and CCL3
2X6G 2.18 Å, X-ray Structure of Macrophage Inflammatory Protein-1 alpha (D27A)
5COR 2.55 Å, X-ray structure of macrophage inflammatory protein-1 alpha (CCL3) N-terminal-switch…
4RA8 2.6 Å, Structure analysis of the Mip1a P8A mutant
7F1T 2.6 Å, Crystal structure of the human chemokine receptor CCR5 in complex with MIP-1a
2X69 2.65 Å, X-ray Structure of Macrophage Inflammatory Protein-1 alpha polymer
3KBX 2.65 Å, Human macrophage inflammatory protein-1 alpha L3M_V63M
4ZKB 2.9 Å, The chemokine binding protein of orf virus complexed with CCL3
7F1Q 2.9 Å, Cryo-EM structure of the chemokine receptor CCR5 in complex with MIP-1a and Gi
3H44 3.0 Å, Crystal Structure of Insulin Degrading Enzyme in Complex with macrophage inflammatory…
1B50 NMR structure of human mip-1A D26A, 10 structures
1B53 NMR structure of human mip-1A D26A, minimized average structure

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