3D87: Interleukin-23

Name: PDB 3D87: Crystal structure of Interleukin-23
Published: 2008-09-02
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: cytokine

Crystal structure of Interleukin-23. Determined by X-ray diffraction at 2.9 Å resolution. Released 2 Sept 2008.

Method: X-ray diffraction
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,104
Mol. weight: 109.29 kDa
Ligands: PO4, MAN
Released: 2 Sept 2008

Explore 3D87 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D87 contains 23 α-helices and 68 β-strands across 4 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
α-helix	11-24	14
β-strand	29	1	1
β-strand	33	1	1
α-helix	54-56	3
α-helix	60-65	6
α-helix	68-86	19
α-helix	101-116	16
α-helix	136-167	32

Chain B: 3 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	2
β-strand	8-13	6	2
β-strand	22-27	6	3
β-strand	37-40	4	4
β-strand	49	1	4
β-strand	52-57	6	3
α-helix	60-62	3
β-strand	64-65	2	2
β-strand	66-70	5	4
β-strand	73-76	4	4
β-strand	79-84	6	2
β-strand	85-86	2	5
β-strand	89-90	2	5
β-strand	95-96	2	2
β-strand	108-110	3	2
β-strand	111	1	6
β-strand	117-124	8	2
β-strand	130-138	9	2
β-strand	145-148	4	2
β-strand	152-158	7	2
β-strand	163-173	11	2
β-strand	186-194	9	2
β-strand	197-205	9	2
α-helix	207-209	3
β-strand	211	1	6
α-helix	213-216	4
β-strand	217-220	4	7
β-strand	223-225	3	7
β-strand	227-235	9	7
β-strand	249-254	6	8
β-strand	266-269	4	8
β-strand	273-276	4	7
β-strand	280	1	9
β-strand	282	1	9
β-strand	283-290	8	8
β-strand	301-304	4	8

Chain C: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	11-27	17
α-helix	54-56	3
α-helix	60-64	5
α-helix	68-86	19
α-helix	88-91	4
α-helix	101-114	14
α-helix	136-163	28
α-helix	164-168	5

Chain D: 5 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	10
β-strand	8-13	6	10
β-strand	22	1	11
β-strand	25-27	3	12
β-strand	36-40	5	10
β-strand	48-49	2	10
β-strand	52-54	3	12
β-strand	57	1	11
α-helix	60-62	3
β-strand	64-70	7	10
β-strand	77-84	8	10
β-strand	85-86	2	13
β-strand	89-90	2	13
β-strand	108-110	3	14
β-strand	111	1	15
β-strand	117-124	8	14
β-strand	132-138	7	14
α-helix	143	1
β-strand	144-153	10	14
β-strand	158	1	16
β-strand	163	1	16
β-strand	165-173	9	14
β-strand	186-192	7	14
β-strand	197	1	10
β-strand	199-205	7	14
α-helix	207-210	4
β-strand	211	1	15
α-helix	214-216	3
β-strand	220-223	4	17
β-strand	229-233	5	17
β-strand	249-251	3	18
β-strand	253	1	19
β-strand	267	1	19
β-strand	273-277	5	17
β-strand	285	1	20
β-strand	288-290	3	18
α-helix	296-298	3
β-strand	302	1	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-23 subunit p19	A, C	protein	178	Homo sapiens	Q9NPF7 (AlphaFold model)
Interleukin-12 subunit p40	B, D	protein	306	Homo sapiens	P29460 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>3D87_1 Interleukin-23 subunit p19 (chains A, C)
RAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEGDEETTNDVPHIQCGDGCDP
QGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQPEG
HHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATLSPGSHHHHHH

Sequence of entity 2 (B, D), FASTA

>3D87_2 Interleukin-12 subunit p40 (chains B, D)
IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEF
GDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTC
WWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAA
EESLPIEVMVDAVHKLKYEQYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW
STPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEW
ASVPCS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2
MAN	alpha-D-mannopyranose	C6 H12 O6	1

Water and common crystallization additives (K) are not listed.

Primary citation

Crystal structures of the pro-inflammatory cytokine interleukin-23 and its complex with a high-affinity neutralizing antibody. Beyer, B.M., Ingram, R., Ramanathan, L. et al. J Mol Biol (2008) 382:942-955. DOI 10.1016/j.jmb.2008.08.001 · PubMed

Other PDB entries of the same protein (UniProt Q9NPF7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5MJ3 1.74 Å, Interleukin-23 complex with an antagonistic alphabody, crystal form 1
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
8CR8 2.0 Å, human Interleukin-23
3DUH 2.3 Å, Structure of Interleukin-23
8UUI 2.43 Å, X-ray structure of Interleukin-23 in complex with peptide 23-446
5MXA 2.5 Å, Structure of unbound Interleukin-23
4GRW 2.55 Å, Structure of a complex of human IL-23 with 3 Nanobodies (Llama vHHs)
6UIB 2.74 Å, Crystal structure of IL23 bound to peptide 23-652
5MZV 2.8 Å, IL-23:IL-23R:Nb22E11 complex
3QWR 3.25 Å, Crystal structure of IL-23 in complex with an adnectin
5MJ4 3.4 Å, Interleukin-23 complex with an antagonistic alphabody, crystal form 2
6WDQ 3.4 Å, IL23/IL23R/IL12Rb1 signaling complex

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