6WGL: Dupilumab fab with Crystal Kappa design

Dupilumab fab with Crystal Kappa design complexed with human IL-4 receptor. Determined by X-ray diffraction at 2.82 Å resolution. Released 16 Sept 2020.

Method: X-ray diffraction
Resolution: 2.82 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,743
Mol. weight: 75.02 kDa
Ligands: NAG
Released: 16 Sept 2020

Explore 6WGL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WGL contains 21 α-helices and 64 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, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	1
β-strand	11-12	2	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	32-39	8	3
β-strand	45-51	7	3
β-strand	58-60	3	3
α-helix	62-64	3
β-strand	70-73	4	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	3
β-strand	108	1	3
β-strand	115	1	3
β-strand	119-121	3	3
β-strand	122-123	2	2
β-strand	129	1	4
β-strand	132-136	5	5
β-strand	147-157	11	5
β-strand	158	1	4
β-strand	163-166	4	6
β-strand	176-177	2	5
α-helix	178-180	3
β-strand	181-182	2	5
β-strand	188-197	10	5
α-helix	199-201	3
β-strand	207-212	6	6
α-helix	213-215	3
β-strand	217-222	6	6

Chain B: 10 helices, 23 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	30-32	3	9
β-strand	35-36	2	9
β-strand	38-43	6	8
α-helix	48-49	2
β-strand	50-54	5	8
β-strand	58-59	2	8
α-helix	60	1
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-95	7	8
α-helix	101	1
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	150-155	6	12
β-strand	158-159	2	12
β-strand	164-168	5	11
α-helix	169-172	4
β-strand	178-187	10	11
α-helix	188-193	6
β-strand	196-203	8	12
β-strand	206-213	8	12

Chain C: 5 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	2-11	10	13
β-strand	16-24	9	13
α-helix	29-32	4
β-strand	33-39	7	14
β-strand	47-49	3	14
β-strand	52-53	2	13
β-strand	58-64	7	13
β-strand	74-80	7	14
β-strand	83-90	8	14
α-helix	92-94	3
β-strand	96	1	13
α-helix	98-101	4
β-strand	105	1	15
β-strand	116-117	2	15
α-helix	127-130	4
β-strand	132-137	6	16
β-strand	149-152	4	16
β-strand	158-159	2	15
β-strand	174	1	17
β-strand	175-180	6	16
β-strand	185	1	13
α-helix	187-192	6
β-strand	194	1	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Dupilumab Fab heavy chain	A	protein	234	Homo sapiens
Dupilumab Fab light chain	B	protein	217	Homo sapiens
Interleukin-4 receptor subunit alpha	C	protein	218	Homo sapiens	P24394 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6WGL_1 Dupilumab Fab heavy chain (chains A)
EVQLVESGGGLEQPGGSLRLSCAGSGFTFRDYAMTWVRQAPGKGLEWVSSISGSGGNTYY
ADSVKGRFTISRDNSKNTLYLQMNSLRAEDTAVYYCAKDRLSITIRPRYYGLDVWGQGTT
VTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPA
VLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGHHHHHH

Sequence of entity 2 (B), FASTA

>6WGL_2 Dupilumab Fab light chain (chains B)
DIVMTQSPLSLPVTPGEPASISCRSSQSLLYSIGYNYLDWYLQKSGQSPQLLIYLGSNRA
SGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYCMQALQTPYTFGQGTKLEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTQGTTSVTKSFNRGEC

Sequence of entity 3 (C), FASTA

>6WGL_3 Interleukin-4 receptor subunit alpha (chains C)
MKVLQEPTCVSDYMSISTCEWKMNGPTNCSTELRLLYQLVFLLSEAHTCIPENNGGAGCV
CHLLMDDVVSADNYTLDLWAGQQLLWKGSFKPSEHVKPRAPGNLTVHTNVSDTLLLTWSN
PYPPDNYLYNHLTYAVNIWSENDPADFRIYNVTYLEPSLRIAASTLKSGISYRARVRAWA
QLYNTTWSEWSPSTKWHNSYREPFEQHGGGGSHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Rapid and robust antibody Fab fragment crystallization utilizing edge-to-edge beta-sheet packing. Lieu, R., Antonysamy, S., Druzina, Z. et al. PLoS One (2020) 15:e0232311-e0232311. DOI 10.1371/journal.pone.0232311 · PubMed

Other PDB entries of the same protein (UniProt P24394 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1IAR 2.3 Å, Interleukin-4 / receptor alpha chain complex
8K4Q 2.59 Å, Crystal structure of nanobody HuNb103 bound to human interleukin-4 receptor subunit alpha
3BPL 2.93 Å, Crystal structure of the IL4-IL4R-Common Gamma ternary complex
3BPO 3.0 Å, Crystal structure of the IL13-IL4R-IL13Ra ternary complex
5E4E 3.0 Å, Engineered Interleukin-13 bound to receptor
3BPN 3.02 Å, Crystal structure of the IL4-IL4R-IL13Ra ternary complex
6OEL 3.1 Å, Engineered Fab bound to IL-4 receptor
8Z8L 3.96 Å, structure of IL-4Ra in complex with an nanobody 4E9
1IRS Irs-1 ptb domain complexed with a il-4 receptor phosphopeptide, NMR, minimized average…

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