5E4E: Engineered Interleukin-13

Engineered Interleukin-13 bound to receptor. Determined by X-ray diffraction at 3.0 Å resolution. Released 2 Dec 2015.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,723
Mol. weight: 73.36 kDa
Ligands: NAG
Released: 2 Dec 2015

Explore 5E4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5E4E contains 14 α-helices and 42 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 A: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	28-31	4
β-strand	33-35	3	1
α-helix	43-51	9
α-helix	61-67	7
α-helix	80-83	4
β-strand	89-91	3	1
α-helix	92-109	18

Chain B: 3 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	8-14	7	2
β-strand	16-22	7	2
β-strand	33-39	7	3
β-strand	47-49	3	3
β-strand	52-53	2	2
β-strand	58-64	7	2
β-strand	74-80	7	3
β-strand	83-90	8	3
β-strand	96	1	2
α-helix	98-101	4
β-strand	102-106	5	4
β-strand	114-119	6	4
α-helix	128-130	3
β-strand	132-139	8	5
β-strand	148-152	5	5
β-strand	158-161	4	4
β-strand	173-180	8	5
α-helix	186-193	8
β-strand	194-195	2	5

Chain C: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	33-35	3
β-strand	36-43	8	6
β-strand	47-53	7	6
β-strand	65-70	6	1
β-strand	74-79	6	1
β-strand	83-87	5	6
β-strand	94-101	8	1
β-strand	113-118	6	1
α-helix	120-122	3
β-strand	130-137	8	7
β-strand	141-147	7	7
β-strand	158-163	6	8
β-strand	171-173	3	8
β-strand	176-179	4	7
β-strand	182-188	7	7
β-strand	201-208	8	8
β-strand	216-221	6	8
β-strand	226-227	2	7
β-strand	232-239	8	9
β-strand	242-248	7	9
α-helix	255-257	3
β-strand	258-266	9	10
β-strand	272-277	6	10
α-helix	285-287	3
β-strand	294-299	6	9
β-strand	308-316	9	10
β-strand	327	1	10
α-helix	328-333	6
β-strand	334-336	3	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Interleukin-13	A	protein	113	Homo sapiens	P35225 (AlphaFold model)
Interleukin-4 receptor subunit alpha	B	protein	203	Homo sapiens	P24394 (AlphaFold model)
Interleukin-13 receptor subunit alpha-1	C	protein	318	Homo sapiens	P78552 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5E4E_1 Interleukin-13 (chains A)
PGPVPPSTAVRELIEELINITQNQKAPLCNGSMVWSINRTAGMYCAALESLINVSGCSAI
EKTQRMLSGFCPHKVSAGQFSSLHVRSSKIEVAQFVKDLLFHLRTLFREGQFN

Sequence of entity 2 (B), FASTA

>5E4E_2 Interleukin-4 receptor subunit alpha (chains B)
MKVLQEPTCVSDYMSISTCEWKMNGPTNCSTELRLLYQLVFLLSEAHTCIPENNGGAGCV
CHLLMDDVVSADNYTLDLWAGQQLLWKGSFKPSEHVKPRAPGNLTVHTNVSDTLLLTWSN
PYPPDNYLYNHLTYAVNIWSENDPADFRIYNVTYLEPSLRIAASTLKSGISYRARVRAWA
QCYNTTWSEWSPSTKWHNSYREP

Sequence of entity 3 (C), FASTA

>5E4E_3 Interleukin-13 receptor subunit alpha-1 (chains C)
GGGAAPTETQPPVTNLSVSVENLCTVIWTWNPPEGASSNCSLWYFSHFGDKQDKKIAPET
RRSIEVPLNERICLQVGSQCSTNESEKPSILVEKCISPPEGDPESAVTELQCIWHNLSYM
KCSWLPGRNTSPDTNYTLYYWHRSLEKIHQCENIFREGQYFGCSFDLTKVKDSSFEQHSV
QIMVKDNAGKIKPSFNIVPLTSRVKPDPPHIKNLSFHNDDLYVQWENPQNFISRCLFYEV
EVNNSQTETHNVFYVQEAKCENPEFERNVENTSCFMVPGVLPDTLNTVRIRVKTNKLCYE
DDKLWSNWSQEMSIGKKR

Ligands and cofactors

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

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

Primary citation

Instructive roles for cytokine-receptor binding parameters in determining signaling and functional potency. Moraga, I., Richter, D., Wilmes, S. et al. Sci Signal (2015) 8:ra114-ra114. DOI 10.1126/scisignal.aab2677 · PubMed

Other PDB entries of the same protein (UniProt P35225 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3L5X 1.9 Å, Crystal structure of the complex between IL-13 and H2L6 FAB
4I77 1.9 Å, Lebrikizumab Fab bound to IL-13
5L6Y 1.99 Å, il13 in complex with tralokinumab
3L5W 2.0 Å, Crystal structure of the complex between IL-13 and C836 FAB
4PS4 2.8 Å, Crystal structure of the complex between IL-13 and M1295 FAB
3BPO 3.0 Å, Crystal structure of the IL13-IL4R-IL13Ra ternary complex
3LB6 3.05 Å, The structure of IL-13 in complex with IL-13Ralpha2
3G6D 3.2 Å, Crystal structure of the complex between CNTO607 Fab and IL-13
8BLQ 3.97 Å, Cryo-EM structure of the CODV-IL13-RefAb triple complex
1GA3 NMR structure of interleukin-13
1IJZ Solution Structure of Human IL-13
1IK0 Solution Structure of Human IL-13

Browse structure collections

About this viewer

MolViewer shows 5E4E directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.