6OEL: Engineered Fab

Engineered Fab bound to IL-4 receptor. Determined by X-ray diffraction at 3.1 Å resolution. Released 7 Aug 2019.

Method: X-ray diffraction
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 5
Atoms: 7,209
Mol. weight: 111.32 kDa
Ligands: NAG
Released: 7 Aug 2019

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

Secondary structure: helices and β-sheets

6OEL contains 28 α-helices and 79 β-strands across 5 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: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-17	12
α-helix	24-26	3
β-strand	28-30	3	1
α-helix	41-59	19
α-helix	70-94	25
β-strand	106-108	3	1
α-helix	109-126	18

Chain B: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
α-helix	6-7	2
β-strand	8-11	4	3
β-strand	16-22	7	3
β-strand	23	1	2
α-helix	29-32	4
β-strand	33-39	7	4
β-strand	47-49	3	4
β-strand	52-53	2	3
β-strand	58-64	7	3
β-strand	74-80	7	4
β-strand	83-90	8	4
α-helix	92-94	3
β-strand	96	1	3
α-helix	98-101	4
β-strand	102-107	6	5
β-strand	113-119	7	5
α-helix	129-131	3
β-strand	132-140	9	6
β-strand	147-152	6	6
β-strand	158-162	5	5
α-helix	163-165	3
β-strand	171-180	10	6
α-helix	181-183	3
α-helix	187-193	7
β-strand	194-197	4	6

Chain C: 2 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	42-43	2	7
β-strand	47-51	5	7
β-strand	68-69	2	8
β-strand	82-84	3	7
β-strand	92-95	4	7
β-strand	106-107	2	8
β-strand	123-124	2	8
β-strand	130	1	7
α-helix	133-135	3
β-strand	136-141	6	9
β-strand	149-153	5	9
β-strand	161-169	9	10
β-strand	176-180	5	10
β-strand	187	1	9
β-strand	197-205	9	10
α-helix	217-221	5
β-strand	222-224	3	10

Chain H: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	11
α-helix	7-9	3
β-strand	11-13	3	12
β-strand	18-26	9	11
β-strand	37-45	9	12
β-strand	49-58	10	12
β-strand	63-67	5	12
β-strand	76-81	6	11
β-strand	86-92	7	11
α-helix	96-98	3
β-strand	100-108	9	12
β-strand	114-118	5	12
β-strand	122-126	5	12
β-strand	132	1	13
β-strand	135-139	5	14
β-strand	150-160	11	14
β-strand	161	1	13
β-strand	166-169	4	15
α-helix	170-172	3
β-strand	174	1	15
β-strand	178-180	3	14
α-helix	181-183	3
β-strand	184-185	2	14
β-strand	191-200	10	14
α-helix	201-203	3
β-strand	210-215	6	15
α-helix	216-218	3
β-strand	220-225	6	15

Chain L: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	16
β-strand	10-14	5	17
β-strand	19-25	7	16
β-strand	39-44	6	17
β-strand	51-55	5	17
β-strand	66-67	2	17
α-helix	68	1
β-strand	76-80	5	16
β-strand	86-91	6	16
α-helix	96-98	3
β-strand	100-106	7	17
α-helix	116	1
β-strand	117	1	12
β-strand	118	1	17
β-strand	123-127	5	17
β-strand	131	1	18
β-strand	134-138	5	19
α-helix	139-141	3
α-helix	142-145	4
β-strand	149-159	11	19
β-strand	160	1	18
β-strand	165-170	6	20
β-strand	174	1	20
β-strand	179-183	5	19
α-helix	184-187	4
β-strand	193-202	10	19
α-helix	203-207	5
β-strand	211-217	7	20
β-strand	225-230	6	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
engineered Interleukin-4, RGA variant	A	protein	129	Homo sapiens	P05112 (AlphaFold model)
Interleukin-4 receptor subunit alpha	B	protein	202	Homo sapiens	P24394 (AlphaFold model)
Cytokine receptor common subunit gamma	C	protein	189	Homo sapiens	P31785 (AlphaFold model)
engineered Fab heavy chain	H	protein	229	Homo sapiens
engineered Fab light chain	L	protein	224	Homo sapiens

Sequence of entity 1 (A), FASTA

>6OEL_1 engineered Interleukin-4, RGA variant (chains A)
HKCDITLQEIIKTLNSLTEQKTLCTELTVTDIFAASKNTTEKETFCRAATVLRQFYSHHE
KDTRCLGATAQQFHRHKQLIRFLKRLDRNLWGLAGLNSCPVKEANQSTLENFLERLRVIM
QSKWFKCGA

Sequence of entity 2 (B), FASTA

>6OEL_2 Interleukin-4 receptor subunit alpha (chains B)
ADPFKVLQEPTCVSDYMSISTCEWKMNGPTNCSTELRLLYQLVFLLSEAHTCIPENNGGA
GCVCHLLMDDVVSADNYTLDLWAGQQLLWKGSFKPSEHVKPRAPGNLTVHTNVSDTLLLT
WSNPYPPDNYLYNHLTYAVNIWSENDPADFRIYNVTYLEPSLRIAASTLKSGISYRARVR
AWAQCYNTTWSEWSPSTKWHNS

Sequence of entity 3 (C), FASTA

>6OEL_3 Cytokine receptor common subunit gamma (chains C)
QCFVFNVEYMNCTWQSSSEPQPTNLTLHYWYKNSDNDKVQKCSHYLFSEEITSGCQLQKK
EIHLYQTFVVQLQDPREPRRQATQMLKLQNLVIPWAPENLTLHKLSESQLELNWNNRFLN
HCLEHLVQYRTDWDHSWTEQSVDYRHKFSLPSVDGQKRYTFRVRSRFNPLCGSAQHWSEW
SHPIHWGSN

Sequence of entity 4 (H), FASTA

>6OEL_4 engineered Fab heavy chain (chains H)
QVQLQQSGPGLVKPSQTLSLTCAISGDSVSSNIATWNWIRQSPSRGLEWLGRTYYRSKWY
NDYAVSVRSRISISPDTSKNQFSLQLNSVTPEDTAIYYCARFSGWLGTGDCWGQGTLVTV
SSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQ
SSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVCSRLEVLFQ

Sequence of entity 5 (L), FASTA

>6OEL_5 engineered Fab light chain (chains L)
DIQVTQSPSSLSASVGDRVTITCRASQGISTWLAWYQQRPGKAPKLLIYAASSLETGVPS
RFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPWTFGQGTKVEIKRTVAAPSVFIFPP
SDSQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGECSRGGLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	5

Water and common crystallization additives (NO3) are not listed.

Primary citation

A strategy for the selection of monovalent antibodies that span protein dimer interfaces. Spangler, J.B., Moraga, I., Jude, K.M. et al. J Biol Chem (2019) 294:13876-13886. DOI 10.1074/jbc.RA119.009213 · PubMed

Other PDB entries of the same protein (UniProt P05112 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2D48 1.65 Å, Crystal structure of the Interleukin-4 variant T13D
2B8X 1.7 Å, Crystal structure of the interleukin-4 variant F82D
2B8U 1.8 Å, Crystal structure of wildtype human Interleukin-4
2B8Y 1.8 Å, Crystal structure of the interleukin-4 variant T13DF82D
2B91 2.0 Å, Crystal structure of the interleukin-4 variant F82DR85A
4YDY 2.0 Å, Crystal structure of darpin 44C12V5 in complex with human il-4
1HZI 2.05 Å, Interleukin-4 mutant E9A
2B90 2.1 Å, Crystal structure of the interleukin-4 variant T13DR85A
1RCB 2.25 Å, Crystal structure of human recombinant interleukin-4 at 2.25 Å resolution
1IAR 2.3 Å, Interleukin-4 / receptor alpha chain complex
2INT 2.35 Å, Crystal structure of recombinant human interleukin-4
2B8Z 2.5 Å, Crystal structure of the interleukin-4 variant R85A

Browse structure collections

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