4NI9: Human interleukin 6

Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer (SOMAMER SL1025), FORM 2. Determined by X-ray diffraction at 2.55 Å resolution. Released 22 Jan 2014.

Method: X-ray diffraction
Resolution: 2.55 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,793
Mol. weight: 65.13 kDa
Released: 22 Jan 2014

Explore 4NI9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NI9 contains 14 α-helices and 0 β-strands across 2 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	17-20	4
α-helix	21-40	20
α-helix	69-71	3
α-helix	80-102	23
α-helix	109-129	21
α-helix	142-151	10
α-helix	156-181	26

Chain C: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	21-42	22
α-helix	69-71	3
α-helix	80-99	20
α-helix	102-105	4
α-helix	109-128	20
α-helix	144-151	8
α-helix	156-181	26

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
SOMAmer SL1025	B, D	DNA	32
Interleukin-6	A, C	protein	186	Homo sapiens	P05231 (AlphaFold model)

Sequence of entity 1 (B, D), FASTA

>4NI9_1 SOMAmer SL1025 (chains B, D)
GGCAGGXXXGGXAXXAACACGXXAAGXCGXGG

Sequence of entity 2 (A, C), FASTA

>4NI9_2 Interleukin-6 (chains A, C)
MAPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALA
ENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMS
TKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSL
RALRQM

Primary citation

Crystal structure of interleukin-6 in complex with a modified nucleic Acid ligand. Gelinas, A.D., Davies, D.R., Edwards, T.E. et al. J Biol Chem (2014) 289:8720-8734. DOI 10.1074/jbc.M113.532697 · PubMed

Other PDB entries of the same protein (UniProt P05231 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1ALU 1.9 Å, Human interleukin-6
7NXZ 2.0 Å, Synthetic glycoform of Human Interleukin 6
4CNI 2.2 Å, Crystal structure of the Fab portion of Olokizumab in complex with IL- 6
4J4L 2.3 Å, Modular evolution and design of the protein binding interface
4NI7 2.4 Å, Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer…
4O9H 2.42 Å, Structure of Interleukin-6 in complex with a Camelid Fab fragment
8YWQ 2.51 Å, Crystal structure of the Fab fragment of the anti-IL-6 antibody I9H in complex with a…
5FUC 2.7 Å, Biophysical and cellular characterisation of a junctional epitope antibody that locks…
4ZS7 2.93 Å, Structural mimicry of receptor interaction by antagonistic IL-6 antibodies
8YWR 2.93 Å, Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a…
8QY5 3.1 Å, Structure of interleukin 6.
8QY6 3.16 Å, Structure of interleukin 6 (gp130 P496L mutant).

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