3HMX: Ustekinumab FAB/IL-12 complex

Crystal structure of ustekinumab FAB/IL-12 complex. Determined by X-ray diffraction at 3.0 Å resolution. Released 9 Jun 2010.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,078
Mol. weight: 106.06 kDa
Released: 9 Jun 2010

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

Secondary structure: helices and β-sheets

3HMX contains 27 α-helices and 72 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, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	8-14	7	1
β-strand	22-27	6	2
α-helix	28	1
β-strand	37-40	4	1
β-strand	49	1	1
β-strand	52-57	6	2
α-helix	60-62	3
β-strand	64-69	6	1
β-strand	74-87	14	1
β-strand	89-90	2	1
α-helix	91	1
β-strand	95	1	3
β-strand	107-110	4	3
β-strand	111	1	4
β-strand	117-124	8	3
β-strand	130-138	9	1
β-strand	147-148	2	3
β-strand	152-155	4	3
α-helix	163-164	2
β-strand	165-172	8	3
β-strand	186-194	9	1
β-strand	197-205	9	1
α-helix	207-209	3
β-strand	211	1	4
α-helix	213-216	4
β-strand	231-233	3	5
β-strand	249-253	5	6
β-strand	267-269	3	6
β-strand	273-275	3	5
β-strand	284	1	7
β-strand	286-290	5	6
α-helix	296-300	5
β-strand	303	1	7

Chain B: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	14-36	23
α-helix	99-125	27
α-helix	135-148	14
α-helix	166-196	31

Chain H: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	14
α-helix	7-9	3
β-strand	10-12	3	15
β-strand	18-25	8	14
β-strand	33-39	7	15
β-strand	45-51	7	15
β-strand	58-60	3	15
β-strand	69-73	5	14
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-99	8	15
β-strand	106-109	4	15
β-strand	113-117	5	15
α-helix	120-122	3
β-strand	123	1	16
α-helix	124-125	2
β-strand	126-130	5	17
β-strand	141-151	11	17
β-strand	152	1	16
β-strand	157-160	4	18
α-helix	161-163	3
β-strand	165	1	18
β-strand	169-171	3	17
α-helix	172-174	3
β-strand	175-176	2	17
β-strand	182-191	10	17
α-helix	192-194	3
β-strand	200-206	7	18
α-helix	207-209	3
β-strand	211-217	7	18

Chain L: 8 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
β-strand	62-65	4	8
β-strand	70-75	6	8
α-helix	80-82	3
β-strand	85-90	6	9
α-helix	96	1
β-strand	97-98	2	9
β-strand	102-106	5	9
α-helix	107	1
β-strand	111	1	10
α-helix	112-113	2
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	144-148	5	12
β-strand	149-150	2	13
β-strand	153-154	2	13
β-strand	159-160	2	11
β-strand	163	1	11
β-strand	173-182	10	11
α-helix	183-187	5
β-strand	192-198	7	12
β-strand	205-209	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-12 subunit beta	A	protein	306	Homo sapiens	P29460 (AlphaFold model)
Interleukin-12 subunit alpha	B	protein	197	Homo sapiens	P29459 (AlphaFold model)
Ustekinumab FAB light chain	L	protein	214	Homo sapiens
Ustekinumab FAB heavy chain	H	protein	226	Homo sapiens

Sequence of entity 1 (A), FASTA

>3HMX_1 Interleukin-12 subunit beta (chains A)
IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEF
GDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTC
WWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAERVRGDNKEYEYSVECQEDSACPAA
EESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKNSRQVEVSWEYPDTW
STPHSYFSLTFCVQVQGKSKREKKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEW
ASVPCS

Sequence of entity 2 (B), FASTA

>3HMX_2 Interleukin-12 subunit alpha (chains B)
RNLPVATPDPGMFPCLHHSQNLLRAVSNMLQKARQTLEFYPCTSEEIDHEDITKDKTSTV
EACLPLELTKNESCLNSRETSFITNGSCLASRKTSFMMALCLSSIYEDLKMYQVEFKTMN
AKLLMDPKRQIFLDQNMLAVIDELMQALNFNSETVPQKSSLEEPDFYKTKIKLCILLHAF
RIRAVTIDRVMSYLNAS

Sequence of entity 3 (L), FASTA

>3HMX_3 USTEKINUMAB FAB LIGHT CHAIN (chains L)
DIQMTQSPSSLSASVGDRVTITCRASQGISSWLAWYQQKPEKAPKSLIYAASSLQSGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQYNIYPYTFGQGTKLEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 4 (H), FASTA

>3HMX_4 USTEKINUMAB FAB HEAVY CHAIN (chains H)
EVQLVQSGAEVKKPGESLKISCKGSGYSFTTYWLGWVRQMPGKGLDWIGIMSPVDSDIRY
SPSFQGQVTMSVDKSITTAYLQWNSLKASDTAMYYCARRRPGQGYFDFWGQGTLVTVSSS
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTH

Primary citation

Structural basis for the dual recognition of IL-12 and IL-23 by ustekinumab. Luo, J., Wu, S.J., Lacy, E.R. et al. J Mol Biol (2010) 402:797-812. DOI 10.1016/j.jmb.2010.07.046 · 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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