8YWR: Fab fragment of the anti-IL-6 antibody 68F2

Crystal structure of the Fab fragment of the anti-IL-6 antibody 68F2 in complex with a domain-swapped IL-6 dimer. Determined by X-ray diffraction at 2.93 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 2.93 Å
Organisms: Homo sapiens, Lama glama
Chains: 3
Atoms: 4,283
Mol. weight: 66.63 kDa
Released: 6 Nov 2024

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

Secondary structure: helices and β-sheets

8YWR contains 22 α-helices and 47 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: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	24-46	23
α-helix	69-71	3
α-helix	80-100	21
α-helix	103-105	3
α-helix	109-128	20
α-helix	144-181	38

Chain H: 6 helices, 23 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	48-53	6	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	111-112	2	3
β-strand	116-118	3	3
β-strand	119-120	2	2
α-helix	124-125	2
β-strand	126	1	4
β-strand	129-133	5	5
α-helix	134-136	3
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	195-198	4
β-strand	203-209	7	6
α-helix	210-212	3
β-strand	214-220	7	6

Chain L: 10 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	4	1	7
β-strand	5	1	8
β-strand	9-12	4	9
β-strand	18-23	6	8
α-helix	29-32	4
β-strand	35-40	6	9
β-strand	47-51	5	9
β-strand	55-56	2	9
α-helix	57	1
β-strand	64-69	6	8
β-strand	72-77	6	8
α-helix	82-84	3
β-strand	86-94	9	9
β-strand	98-101	4	9
β-strand	102	1	7
β-strand	105-109	5	9
α-helix	112-114	3
β-strand	115	1	10
α-helix	116-117	2
β-strand	118-122	5	11
α-helix	123-125	3
α-helix	126-130	5
β-strand	134-143	10	11
β-strand	144	1	10
β-strand	149-154	6	12
β-strand	157-158	2	12
α-helix	159	1
β-strand	163-165	3	11
α-helix	166-168	3
β-strand	169-170	2	11
β-strand	176-184	9	11
α-helix	186-191	6
β-strand	195-201	7	12
β-strand	204-210	7	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6	A	protein	171	Homo sapiens	P05231 (AlphaFold model)
Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2	H	protein	222	Lama glama
Light chain of the Fab fragment of anti-IL-6 antibody 68F2	L	protein	216	Lama glama

Sequence of entity 1 (A), FASTA

>8YWR_1 Interleukin-6 (chains A)
PHRQPLTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGC
FQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNL
DAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Sequence of entity 2 (H), FASTA

>8YWR_2 Heavy chain of the Fab fragment of anti-IL-6 antibody 68F2 (chains H)
EVQLQESGPGLVKPSQTLSLTCTVSGGSITTRYYAWSWIRQPPGKGLEWMGVIDYDGDTY
YSPSLKSRTSISWDTSKNQFSLQLSSVTPEDTAVYYCARDPDVVTGFHYDYWGQGTQVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEP

Sequence of entity 3 (L), FASTA

>8YWR_3 Light chain of the Fab fragment of anti-IL-6 antibody 68F2 (chains L)
QAVLTQPPLVSGTPGQTVTISCAGANNDIGTYAYVSWYQQLPGTAPKLLIYKVTTRASGI
PSRFSGSKSGNTASLTISGLQSEDEADYYCASYRNFNNAVFGRGTHLTVLGQPKAAPSVT
LFPPSSEELQANKATLVCLISDFYPGAVTVAWKADSSPVKAGVETTTPSKQSNNKYAASS
YLSLTPEQWKSHRSYSCQVTHEGSTVEKTVAPTECS

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
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
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 8YWR 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.