4O9H: Interleukin-6

Structure of Interleukin-6 in complex with a Camelid Fab fragment. Determined by X-ray diffraction at 2.42 Å resolution. Released 15 Apr 2015.

Method: X-ray diffraction
Resolution: 2.42 Å
Organisms: Homo sapiens, Llama glama
Chains: 3
Atoms: 4,489
Mol. weight: 67.17 kDa
Released: 15 Apr 2015

Explore 4O9H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4O9H contains 20 α-helices and 46 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: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	22-41	20
α-helix	69-71	3
α-helix	80-103	24
α-helix	109-129	21
α-helix	137-140	4
α-helix	141-152	12
α-helix	156-181	26

Chain H: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	34-39	6	3
β-strand	46-51	6	3
β-strand	58-60	3	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-98	7	3
β-strand	101	1	4
β-strand	104	1	4
β-strand	108	1	3
β-strand	112-114	3	3
β-strand	115-116	2	2
α-helix	120-121	2
β-strand	122	1	5
β-strand	125-129	5	6
β-strand	143-150	8	6
β-strand	151	1	5
β-strand	156-159	4	7
β-strand	168-170	3	6
α-helix	171-173	3
β-strand	174-175	2	6
β-strand	181-187	7	6
β-strand	200-205	6	7
α-helix	206-208	3
β-strand	210-215	6	7

Chain L: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-5	2	8
β-strand	9-12	4	9
β-strand	17-22	6	10
β-strand	23-24	2	8
α-helix	31-33	3
β-strand	36-40	5	9
β-strand	47-51	5	9
β-strand	55-56	2	9
α-helix	57	1
β-strand	64-69	6	10
β-strand	72-78	7	10
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	97-100	4	9
β-strand	104-108	5	9
β-strand	114	1	11
α-helix	115-116	2
β-strand	117-121	5	12
α-helix	122-124	3
α-helix	125-129	5
β-strand	133-142	10	12
β-strand	143	1	11
β-strand	148-153	6	13
β-strand	162-164	3	12
β-strand	168-169	2	12
α-helix	171-173	3
β-strand	175-183	9	12
α-helix	185-190	6
β-strand	194-200	7	13
β-strand	203-209	7	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6	A	protein	186	Homo sapiens	P05231 (AlphaFold model)
Heavy Chain of the Camelid Fab fragment 61H7	H	protein	223	Llama glama
Light Chain of the Camelid Fab fragment 61H7	L	protein	215	Llama glama

Sequence of entity 1 (A), FASTA

>4O9H_1 Interleukin-6 (chains A)
MAPVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALA
ENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMS
TKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSL
RALRQM

Sequence of entity 2 (H), FASTA

>4O9H_2 Heavy Chain of the Camelid Fab fragment 61H7 (chains H)
EVQLVESGGGLVQPGGSLRLSCAASGFTFSSYRMYWVRQPPGKGLEWVSAISAGGGSTYY
GDSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCANRAGWGMGDYWGQGTQVTVSSAS
TKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDK

Sequence of entity 3 (L), FASTA

>4O9H_3 Light Chain of the Camelid Fab fragment 61H7 (chains L)
QTVVTQEPSLSVSPGGTVTLTCGLSSGSVTASNYPGWFQQTPGQAPRALIYSTNDRHSGV
PSRFSGSISGNKAALTITGAQPEDEADYYCALDIGDITEFGGGTHLTVLGQPKAAPSVTL
FPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASSY
LSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

Primary citation

Combining residues of naturally-occurring Camelid somatic affinity variants yields ultra-potent human therapeutic IL-6 antibodies. Klarenbeek, A., Blanchetot, C., Schragel, G. et al. To be published.

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…
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…
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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