4ZS7: Interleukin-6

Structural mimicry of receptor interaction by antagonistic IL-6 antibodies. Determined by X-ray diffraction at 2.93 Å resolution. Released 4 May 2016.

Method: X-ray diffraction
Resolution: 2.93 Å
Organisms: Homo sapiens, Lama glama
Chains: 3
Atoms: 4,454
Mol. weight: 66.44 kDa
Released: 4 May 2016

Explore 4ZS7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4ZS7 contains 16 α-helices and 45 β-strands across 3 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, 0 β-strands

Element	Residues	Length
α-helix	26-47	22
α-helix	80-97	18
α-helix	109-129	21
α-helix	141-150	10
α-helix	158-183	26

Chain H: 4 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	11-12	2	2
β-strand	18-24	7	1
β-strand	35-41	7	3
β-strand	48-54	7	3
β-strand	59-61	3	3
β-strand	69-74	6	1
β-strand	79-84	6	1
α-helix	89-91	3
β-strand	93-100	8	3
β-strand	112	1	3
β-strand	116-118	3	3
β-strand	119-120	2	2
β-strand	126	1	4
β-strand	129-136	8	5
β-strand	144-154	11	5
β-strand	155	1	4
β-strand	160-163	4	6
β-strand	168	1	6
β-strand	172-174	3	5
α-helix	175-177	3
β-strand	178-179	2	5
β-strand	185-194	10	5
α-helix	197-199	3
β-strand	203-209	7	6
α-helix	210-212	3
β-strand	214-220	7	6

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	7
β-strand	9-12	4	8
β-strand	18-23	6	7
α-helix	26-30	5
β-strand	36-40	5	8
β-strand	47-51	5	8
β-strand	55-56	2	8
α-helix	57	1
β-strand	64-68	5	7
β-strand	72-77	6	7
α-helix	82-84	3
β-strand	87-94	8	8
β-strand	98-101	4	8
β-strand	105-109	5	8
β-strand	115	1	9
β-strand	118-122	5	10
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	10
β-strand	144	1	9
β-strand	149-154	6	11
β-strand	157-159	3	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-184	9	10
α-helix	186-191	6
β-strand	195-201	7	11
β-strand	204-210	7	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6	A	protein	171	Homo sapiens	P05231 (AlphaFold model)
Llama Fab fragment 68F2 heavy chain	H	protein	222	Lama glama
Llama Fab fragment 68F2 light chain	L	protein	216	Lama glama

Sequence of entity 1 (A), FASTA

>4ZS7_1 Interleukin-6 (chains A)
PHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGC
FQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNL
DAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Sequence of entity 2 (H), FASTA

>4ZS7_2 Llama Fab fragment 68F2 heavy chain (chains H)
EVQLQESGPGLVKPSQTLSLTCTVSGGSITTRYYAWSWIRQPPGKGLEWMGVIDYDGDTY
YSPSLKSRTSISWDTSKNQFSLQLSSVTPEDTAVYYCARDPDVVTGFHYDYWGQGTQVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (L), FASTA

>4ZS7_3 Llama Fab fragment 68F2 light chain (chains L)
QAVLTQPPLVSGTPGQTVTISCAGANNDIGTYAYVSWYQQLPGTAPKLLIYKVTTRASGI
PSRFSGSKSGNTASLTISGLQSEDEADYYCASYRNFNNAVFGRGTHLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Structural Mimicry of Receptor Interaction by Antagonistic Interleukin-6 (IL-6) Antibodies. Blanchetot, C., De Jonge, N., Desmyter, A. et al. J Biol Chem (2016) 291:13846-13854. DOI 10.1074/jbc.M115.695528 · 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…
4NI9 2.55 Å, Crystal structure of human interleukin 6 in complex with a modified nucleotide aptamer…
5FUC 2.7 Å, Biophysical and cellular characterisation of a junctional epitope antibody that locks…
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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