5NJD: Interleukin 23

Structure of Interleukin 23 in complex with Briakinumab FAb. Determined by X-ray diffraction at 3.9 Å resolution. Released 3 Jan 2018.

Method: X-ray diffraction
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 24
Atoms: 39,445
Mol. weight: 701.06 kDa
Released: 3 Jan 2018

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

Secondary structure: helices and β-sheets

5NJD contains 135 α-helices and 438 β-strands across 24 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	1
β-strand	30-36	7	1
β-strand	44-49	6	2
β-strand	59-62	4	1
β-strand	65-71	7	1
β-strand	74-79	6	2
α-helix	82-84	3
β-strand	86-92	7	1
β-strand	95-108	14	1
β-strand	111-112	2	1
β-strand	117	1	1
α-helix	118-119	2
β-strand	130-132	3	1
β-strand	133	1	3
β-strand	139-146	8	1
β-strand	152-160	9	1
β-strand	166-170	5	1
β-strand	174-181	8	1
β-strand	184-195	12	1
α-helix	207	1
β-strand	208-216	9	1
β-strand	219-227	9	1
α-helix	229-232	4
β-strand	233	1	3
α-helix	235-238	4
β-strand	239-245	7	4
β-strand	252-257	6	4
β-strand	271-277	7	5
β-strand	287-291	5	5
β-strand	295-298	4	4
β-strand	305-312	8	5
α-helix	318-322	5
β-strand	323-326	4	5

Chain B: 8 helices, 0 β-strands

Element	Residues	Length
α-helix	30-45	16
α-helix	49-51	3
α-helix	79-84	6
α-helix	87-104	18
α-helix	107-110	4
α-helix	114-116	3
α-helix	121-133	13
α-helix	155-185	31

Chain C: 4 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	6
β-strand	30-37	8	6
β-strand	44-49	6	7
β-strand	59-62	4	6
β-strand	70-71	2	6
β-strand	74-79	6	7
α-helix	82-84	3
β-strand	86-92	7	6
β-strand	95-108	14	6
β-strand	111-112	2	6
β-strand	117	1	6
β-strand	130-132	3	6
β-strand	133	1	8
β-strand	139-146	8	6
β-strand	152-160	9	6
β-strand	167-170	4	6
β-strand	174-180	7	6
β-strand	185-195	11	6
β-strand	208-216	9	6
β-strand	219-227	9	6
α-helix	229-232	4
β-strand	233	1	8
α-helix	235-238	4
β-strand	239-245	7	9
β-strand	252-257	6	9
β-strand	271-278	8	10
β-strand	289-291	3	10
β-strand	295-298	4	9
β-strand	305-312	8	10
α-helix	318-322	5
β-strand	323-326	4	10

Chain D: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	30-45	16
α-helix	79-84	6
α-helix	87-104	18
α-helix	114	1
α-helix	120-135	16
α-helix	155-186	32

Chain E: 6 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	11
β-strand	30-36	7	11
β-strand	44-49	6	12
β-strand	59-62	4	11
β-strand	65-71	7	11
β-strand	74-79	6	12
α-helix	82-84	3
β-strand	86-92	7	11
β-strand	95-108	14	11
β-strand	111-112	2	11
β-strand	117	1	13
β-strand	130-132	3	13
β-strand	133	1	14
β-strand	139-146	8	13
β-strand	152-160	9	11
α-helix	165	1
β-strand	166	1	11
α-helix	167	1
β-strand	168-170	3	13
β-strand	174-180	7	13
β-strand	185-195	11	13
β-strand	208-216	9	11
β-strand	219-227	9	11
α-helix	229-232	4
β-strand	233	1	14
α-helix	235-238	4
β-strand	239-245	7	15
β-strand	251-257	7	15
β-strand	271-277	7	16
β-strand	289-291	3	16
β-strand	295-299	5	15
β-strand	305-312	8	16
α-helix	318-322	5
β-strand	323-326	4	16

Chain F: 7 helices, 0 β-strands

Element	Residues	Length
α-helix	30-44	15
α-helix	79-84	6
α-helix	87-103	17
α-helix	107-110	4
α-helix	114-115	2
α-helix	121-135	15
α-helix	155-186	32

Chain G: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	24-27	4	17
β-strand	30-36	7	17
β-strand	44-49	6	18
β-strand	59-62	4	17
β-strand	70-71	2	17
β-strand	74-79	6	18
α-helix	82-84	3
β-strand	86-92	7	17
β-strand	95-108	14	17
β-strand	111-112	2	17
β-strand	117	1	19
α-helix	118-119	2
β-strand	130-132	3	19
β-strand	133	1	20
β-strand	139-146	8	19
β-strand	152-160	9	17
β-strand	166	1	17
β-strand	168-170	3	19
β-strand	174-180	7	19
β-strand	185-195	11	19
β-strand	208-216	9	17
β-strand	219-227	9	17
α-helix	229-231	3
β-strand	233	1	20
α-helix	235-238	4
β-strand	239-244	6	21
β-strand	252-257	6	21
β-strand	271-277	7	22
β-strand	288-291	4	22
β-strand	295-298	4	21
β-strand	305-312	8	22
α-helix	318-322	5
β-strand	323-326	4	22

Chain H: 6 helices, 0 β-strands

Element	Residues	Length
α-helix	30-45	16
α-helix	79-84	6
α-helix	87-104	18
α-helix	107-110	4
α-helix	121-135	15
α-helix	155-185	31

16 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit beta	A, C, E, G, I, K	protein	328	Homo sapiens	P29460 (AlphaFold model)
Interleukin-23 subunit alpha	B, D, F, H, J, L	protein	198	Homo sapiens	Q9NPF7 (AlphaFold model)
Briakinumab FAb Light chain	M, O, Q, S, U, W	protein	245	Homo sapiens
Briakinumab FAb Heavy chain	N, P, R, T, V, X	protein	289	Homo sapiens

Sequence of entity 1 (A, C, E, G, I, K), FASTA

>5NJD_1 Interleukin-12 subunit beta (chains A, C, E, G, I, K)
MCHQQLVISWFSLVFLASPLVAIWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITW
TLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQ
KEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERV
RGDNKEYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKN
LQLKPLKNSRQVEVSWEYPDTWSTPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVIC
RKNASISVRAQDRYYSSSWSEWASVPCS

Sequence of entity 2 (B, D, F, H, J, L), FASTA

>5NJD_2 Interleukin-23 subunit alpha (chains B, D, F, H, J, L)
MLGSRAVMLLLLLPWTAQGRAVPGGSSPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEG
DEETTNDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSP
VGQLHASLLGLSQLLQPEGHHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVF
AHGAATLSPGTKHHHHHH

Sequence of entity 3 (M, O, Q, S, U, W), FASTA

>5NJD_3 Briakinumab FAb Light chain (chains M, O, Q, S, U, W)
MGILPSPGMPALLSLVSLLSVLLMGCVAQSVLTQPPSVSGAPGQRVTISCSGSRSNIGSN
TVKWYQQLPGTAPKLLIYYNDQRPSGVPDRFSGSKSGTSASLAITGLQAEDEADYYCQSY
DRYTHPALLFGTGTKVTVLGQPKAAPSVTLFPPSSEELQANKATLVCLISDFYPGAVTVA
WKADSSPVKAGVETTTPSKQSNNKYAASSYLSLTPEQWKSHRSYSCQVTHEGSTVEKTVA
PTECS

Sequence of entity 4 (N, P, R, T, V, X), FASTA

>5NJD_4 Briakinumab FAb Heavy chain (chains N, P, R, T, V, X)
MGILPSPGMPALLSLVSLLSVLLMGCVAQVQLVESGGGVVQPGRSLRLSCAASGFTFSSY
GMHWVRQAPGKGLEWVAFIRYDGSNKYYADSVKGRFTISRDNSKNTLYLQMNSLRAEDTA
VYYCKTHGSHDNWGQGTMVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPV
TVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKK
VEPKSCDKGTSGLVPRGSGGSGGSGLNDIFEAQKIEWHEGRTKHHHHHH

Primary citation

Structural Activation of Pro-inflammatory Human Cytokine IL-23 by Cognate IL-23 Receptor Enables Recruitment of the Shared Receptor IL-12R beta 1. Bloch, Y., Bouchareychas, L., Merceron, R. et al. Immunity (2018) 48:45-58.e6. DOI 10.1016/j.immuni.2017.12.008 · PubMed

Other PDB entries of the same protein (UniProt P29460 (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
1F42 2.5 Å, The P40 domain of human interleukin-12
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
1F45 2.8 Å, Human interleukin-12
5MZV 2.8 Å, IL-23:IL-23R:Nb22E11 complex
3D87 2.9 Å, Crystal structure of Interleukin-23

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