8YWQ: Fab fragment of the anti-IL-6 antibody I9H

Crystal structure of the Fab fragment of the anti-IL-6 antibody I9H in complex with a domain-swapped IL-6 dimer. Determined by X-ray diffraction at 2.51 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 2.51 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,270
Mol. weight: 69.34 kDa
Ligands: MG
Released: 6 Nov 2024

Explore 8YWQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8YWQ contains 17 α-helices and 49 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	21-40	20
α-helix	69-71	3
β-strand	73	1	14
β-strand	78	1	14
α-helix	82-130	49
α-helix	141-153	13
α-helix	156-182	27

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
β-strand	35-41	7	3
β-strand	48-54	7	3
β-strand	60-61	2	3
α-helix	66-68	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	111-114	4	3
β-strand	118-120	3	3
β-strand	121-122	2	2
α-helix	126-127	2
β-strand	128	1	4
β-strand	131-135	5	5
β-strand	146	1	6
β-strand	149-156	8	5
β-strand	157	1	4
β-strand	162-165	4	7
β-strand	174-176	3	5
α-helix	177-179	3
β-strand	180-181	2	5
β-strand	187-193	7	5
β-strand	196	1	6
β-strand	206-211	6	7
α-helix	212-214	3
β-strand	216-221	6	7

Chain L: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	8
β-strand	10-13	4	9
β-strand	19-25	7	8
β-strand	33-38	6	9
α-helix	43-44	2
β-strand	45-49	5	9
β-strand	53-54	2	9
α-helix	55	1
β-strand	62-67	6	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	84-90	7	9
β-strand	98	1	9
β-strand	102-106	5	9
β-strand	111	1	10
β-strand	114-118	5	11
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	11
β-strand	140	1	10
β-strand	144-150	7	12
β-strand	153-154	2	12
β-strand	159-163	5	11
α-helix	164-166	3
β-strand	167	1	13
β-strand	172	1	13
β-strand	173-182	10	11
α-helix	183-188	6
β-strand	191-198	8	12
β-strand	206-210	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Heavy chain of the Fab fragment of anti-IL-6 antibody I9H	H	protein	231	Homo sapiens
Light chain of the Fab fragment of anti-IL-6 antibody I9H	L	protein	214	Homo sapiens
Interleukin-6	A	protein	185	Homo sapiens	P05231 (AlphaFold model)

Sequence of entity 1 (H), FASTA

>8YWQ_1 Heavy chain of the Fab fragment of anti-IL-6 antibody I9H (chains H)
QITLKESGPALVKPTQTLTLTCTFSGFSLSTSGMGVGWIRQPPGKALEWLAHIWWDDDKY
YNPSLKSRLTISKDTSKNQVVLTMTNMDPVDTATYYCARRANYGTSYDYGMDYWGQGTLV
TVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTH

Sequence of entity 2 (L), FASTA

>8YWQ_2 Light chain of the Fab fragment of anti-IL-6 antibody I9H (chains L)
DVVMTQSPSSLSASVGDRVTITCKASQSVSDVLTWYQQKPGKAPKLLIYYASNRYTGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQGYRSPYTFGGGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A), FASTA

>8YWQ_3 Interleukin-6 (chains A)
APVPPGEDSKDVAAPHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAE
NNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMST
KVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLR
ALRQM

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structural basis of signaling complex inhibition by IL-6 domain-swapped dimers. Yudenko, A., Bukhdruker, S., Shishkin, P. et al. Structure (2025) 33:171-180.e5. DOI 10.1016/j.str.2024.10.028 · 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
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).

Browse structure collections

About this viewer

MolViewer shows 8YWQ directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.