5FUC: Interleukin-6

Biophysical and cellular characterisation of a junctional epitope antibody that locks IL-6 and gp80 together in a stable complex: implications for new therapeutic strategies. Determined by X-ray diffraction at 2.7 Å resolution. Released 25 Jan 2017.

Method: X-ray diffraction
Resolution: 2.7 Å
Organisms: HOMO SAPIENS, CAMELUS DROMEDARIUS
Chains: 6
Atoms: 7,672
Mol. weight: 120.15 kDa
Ligands: NAG
Released: 25 Jan 2017

Explore 5FUC in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5FUC contains 30 α-helices and 63 β-strands across 6 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	21-45	25
α-helix	69-71	3
α-helix	80-101	22
α-helix	109-127	19
α-helix	138-140	3
α-helix	141-153	13
α-helix	156-182	27

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	22-46	25
α-helix	57-58	2
α-helix	69-71	3
α-helix	80-101	22
α-helix	109-129	21
α-helix	137-140	4
α-helix	141-151	11
α-helix	156-181	26

Chain C: 3 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	1
β-strand	104	1	2
β-strand	111-115	5	1
β-strand	127-134	8	3
β-strand	140	1	3
β-strand	143-145	3	3
β-strand	146-148	3	1
β-strand	155-159	5	1
β-strand	168-175	8	3
β-strand	182	1	3
β-strand	187-190	4	3
α-helix	191-194	4
β-strand	195	1	2
α-helix	197-200	4
β-strand	201-206	6	4
β-strand	215-220	6	4
β-strand	232-240	9	5
β-strand	247-250	4	5
β-strand	257-260	4	4
β-strand	269-277	9	5
β-strand	281	1	5
α-helix	283-290	8
β-strand	291-293	3	5

Chain D: 4 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	101-103	3	6
β-strand	104	1	7
α-helix	110	1
β-strand	111-115	5	6
β-strand	126-132	7	8
β-strand	143-145	3	8
β-strand	146-148	3	6
α-helix	149	1
β-strand	155-159	5	6
β-strand	169-176	8	8
β-strand	181-182	2	8
β-strand	187-189	3	8
β-strand	195	1	7
α-helix	197-200	4
β-strand	201-208	8	9
β-strand	211-220	10	9
β-strand	232-240	9	10
β-strand	247-250	4	10
β-strand	257-260	4	9
β-strand	269-277	9	10
α-helix	286-290	5
β-strand	291-293	3	10

Chain E: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	11
β-strand	21-23	3	11
α-helix	26-31	6
β-strand	33-36	4	12
β-strand	39	1	13
β-strand	45	1	13
β-strand	49-51	3	12
β-strand	58-60	3	12
α-helix	62-64	3
β-strand	68-69	2	14
β-strand	72-73	2	11
β-strand	78-79	2	11
β-strand	82-83	2	14
β-strand	93	1	13
β-strand	96-99	4	12
α-helix	101-103	3
β-strand	114-115	2	12

Chain V: 5 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	15
β-strand	10-12	3	16
β-strand	18-24	7	15
α-helix	26-31	6
β-strand	33-39	7	16
β-strand	46-52	7	16
β-strand	57-60	4	16
β-strand	68-73	6	15
α-helix	74-76	3
β-strand	78-83	6	15
α-helix	88-90	3
β-strand	92-99	8	16
α-helix	101-103	3
α-helix	109-111	3
β-strand	114-115	2	16
β-strand	119-123	5	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-6	A, B	protein	166	HOMO SAPIENS	P05231 (AlphaFold model)
Interleukin-6 receptor subunit alpha, interleukin-6 receptor	C, D	protein	231	HOMO SAPIENS	P08887 (AlphaFold model)
VHH6	E, V	protein	132	CAMELUS DROMEDARIUS

Sequence of entity 1 (A, B), FASTA

>5FUC_1 INTERLEUKIN-6 (chains A, B)
GSSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGF
NEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITT
PDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM

Sequence of entity 2 (C, D), FASTA

>5FUC_2 INTERLEUKIN-6 RECEPTOR SUBUNIT ALPHA, INTERLEUKIN-6 RECEPTOR (chains C, D)
GLAPRRCPAQEVARGAGAGDVPPEEPQLSCFRKSPLSNVVCEWGPRSTPSLTTKAVLLVR
KFQNSPAEDFQEPCQYSQESQKFSCQLAVPEGDSSFYIVSMCVASSVGSKFSKTQTFQGA
GILQPDPPANITVTAVARNPRWLSVTWQDPHSWNSSFYRLRFELRYRAERSKTFTTWMVK
DLQHHAVIHDAWSGLRHVVQLRAQEEFGQGEWSEWSPEAMGTPWTESRSPP

Sequence of entity 3 (E, V), FASTA

>5FUC_3 VHH6 (chains E, V)
DVQFVESGGGSVHAGGSLRLNCATSGYIYSTYCMGWFRQAPGKEREGVAHIYTNSGRTYY
ADSVKGRFTISQDNAKNTVYLQMNSLKPEDTAIYYCAARPSIRCASFSATEYKDWGQGTQ
VTVSSRENLYFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	4

Primary citation

Discovery of a junctional epitope antibody that stabilizes IL-6 and gp80 protein:protein interaction and modulates its downstream signaling. Adams, R., Burnley, R.J., Valenzano, C.R. et al. Sci Rep (2017) 7:37716-37716. DOI 10.1038/srep37716 · 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…
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

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