5M5E: Interleukin-2 variant

Crystal structure of a interleukin-2 variant in complex with interleukin-2 receptor. Determined by X-ray diffraction at 2.3 Å resolution. Released 3 May 2017.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,636
Mol. weight: 78.1 kDa
Ligands: CYS, MAN, NAG
Released: 3 May 2017

Explore 5M5E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M5E contains 22 α-helices and 36 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 B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	7-12	6	1
β-strand	17-23	7	1
α-helix	28-29	2
β-strand	33-39	7	2
β-strand	46-49	4	2
β-strand	51-52	2	1
β-strand	57-63	7	1
β-strand	78-86	9	2
β-strand	89-98	10	2
α-helix	100-102	3
β-strand	104	1	1
α-helix	106-109	4
β-strand	110-117	8	3
β-strand	122-127	6	3
α-helix	133-135	3
β-strand	139-146	8	4
α-helix	156-157	2
β-strand	158-160	3	4
β-strand	166-169	4	3
α-helix	172-173	2
β-strand	177-186	10	4
α-helix	194-200	7
β-strand	201-204	4	4

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	35-38	4
β-strand	39-43	5	5
β-strand	47-51	5	5
β-strand	64-69	6	6
α-helix	77	1
β-strand	78-79	2	6
α-helix	80	1
β-strand	83-86	4	5
β-strand	89-96	8	5
α-helix	97-99	3
α-helix	105	1
β-strand	106-111	6	6
β-strand	119-124	6	6
α-helix	126-128	3
β-strand	130-131	2	5
α-helix	132-135	4
β-strand	136-144	9	7
β-strand	147-153	7	7
α-helix	158-160	3
β-strand	162-169	8	8
β-strand	176-180	5	8
β-strand	185-188	4	7
β-strand	197-204	8	8
α-helix	214-221	8
β-strand	222-224	3	8

Chain D: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	5-28	24
β-strand	44	1	9
β-strand	47	1	10
α-helix	53-56	4
α-helix	57-60	4
α-helix	63-72	10
α-helix	82-97	16
β-strand	107	1	10
β-strand	112	1	9
α-helix	114-132	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-2 receptor subunit beta	B	protein	233	Homo sapiens	P14784 (AlphaFold model)
Cytokine receptor common subunit gamma	C	protein	259	Homo sapiens	P31785 (AlphaFold model)
Interleukin-2	D	protein	160	Homo sapiens	P60568 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>5M5E_1 Interleukin-2 receptor subunit beta (chains B)
AVNGTSQFTCFYNSRANISCVWSQDGALQDTSCQVHAWPDRRRWNQTCELLPVSQASWAC
NLILGAPDSQKLTTVDIVTLRVLCREGVRWRVMAIQDFKPFENLRLMAPISLQVVHVETH
RCNISWEISQASHYFERHLEFEARTLSPGHTWEEAPLLTLKQKQEWICLETLTPDTQYEF
QVRVKPLQGEFTTWSPWSQPLAFRTKPAALGKDTGAQDKTHTCPPCPAPELLG

Sequence of entity 2 (C), FASTA

>5M5E_2 Cytokine receptor common subunit gamma (chains C)
LNTTILTPNGNEDTTADFFLTTMPTDSLSVSTLPLPEVQCFVFNVEYMNCTWNSSSEPQP
TNLTLHYWYKNSDNDKVQKCSHYLFSEEITSGCQLQKKEIHLYQTFVVQLQDPREPRRQA
TQMLKLQNLVIPWAPENLTLHKLSESQLELNWNNRFLNHCLEHLVQYRTDWDHSWTEQSV
DYRHKFSLPSVDGQKRYTFRVRSRFNPLCGSAQHWSEWSHPIHWGSNTSKENPFLFALEA
GAQDKTHTCPPCPAPELLG

Sequence of entity 3 (D), FASTA

>5M5E_3 Interleukin-2 (chains D)
MGWSCIILFLVATATGVHSAPASSSTKKTQLQLEHLLLDLQMILNGINNYKNPKLTRMLT
AKFAMPKKATELKHLQCLEEELKPLEEVLNGAQSKNFHLRPRDLISNINVIVLELKGSET
TFMCEYADETATIVEFLNRWITFAQSIISTLTVDHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
CYS	Cysteine	C3 H7 N O2 S	1
MAN	alpha-D-mannopyranose	C6 H12 O6	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines. Klein, C., Waldhauer, I., Nicolini, V.G. et al. Oncoimmunology (2017) 6:e1277306-e1277306. DOI 10.1080/2162402X.2016.1277306 · PubMed

Other PDB entries of the same protein (UniProt P14784 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E8K 1.71 Å, Legionella Longbeachae LeSH (Llo2327) bound to the human interleukin-2 receptor beta…
7S2S 1.93 Å, nanobody bound to Interleukin-2Rbeta
2B5I 2.3 Å, cytokine receptor complex
4GS7 2.35 Å, Structure of the Interleukin-15 quaternary complex
9KMC 2.97 Å, Cryo-EM structure of the heterotrimeric interleukin-2 receptor in complex with…
2ERJ 3.0 Å, Crystal structure of the heterotrimeric interleukin-2 receptor in complex with…
3QAZ 3.8 Å, IL-2 mutant D10 ternary complex

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