5KN5: Epiregulin Antibody LY3016859 Fab Heavy Chain

TGFalpha/Epiregulin complex with neutralizing antibody LY3016859. Determined by X-ray diffraction at 2.8 Å resolution. Released 31 Aug 2016.

Method: X-ray diffraction
Resolution: 2.8 Å
Organism: Homo sapiens
Chains: 6
Atoms: 7,284
Mol. weight: 103.36 kDa
Ligands: ZN
Released: 31 Aug 2016

Explore 5KN5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KN5 contains 33 α-helices and 102 β-strands across 6 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, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
α-helix	7-9	3
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-52	7	2
β-strand	57-60	4	2
α-helix	62-64	3
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-99	8	2
β-strand	107-108	2	2
β-strand	112-116	5	2
β-strand	122	1	3
β-strand	125-129	5	4
β-strand	140-150	11	4
β-strand	151	1	3
β-strand	156-159	4	5
β-strand	164	1	5
β-strand	168-170	3	4
α-helix	171-173	3
β-strand	174-175	2	4
β-strand	181-190	10	4
α-helix	192-195	4
β-strand	199-205	7	5
α-helix	206-208	3
β-strand	210-216	7	5

Chain B: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	6
β-strand	10-13	4	7
β-strand	19-25	7	6
β-strand	38-43	6	7
β-strand	50-54	5	7
β-strand	58-59	2	7
α-helix	60	1
β-strand	67-72	6	6
β-strand	75-80	6	6
α-helix	85-87	3
β-strand	90-95	6	7
β-strand	99	1	8
α-helix	101	1
β-strand	102-103	2	7
β-strand	107-111	5	7
β-strand	116	1	9
α-helix	117-118	2
β-strand	119-123	5	10
α-helix	124-126	3
α-helix	127-132	6
β-strand	134-144	11	10
β-strand	145	1	9
β-strand	150-155	6	11
β-strand	158-159	2	11
β-strand	164-168	5	10
α-helix	169-172	4
β-strand	178-187	10	10
α-helix	188-191	4
β-strand	196-202	7	11
β-strand	210-215	6	11

Chain C: 1 helix, 5 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	12
β-strand	29-34	6	12
α-helix	35	1
β-strand	38-39	2	13
β-strand	45-46	2	13
β-strand	47	1	8

Chain D: 9 helices, 23 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
α-helix	29-31	3
β-strand	33-39	7	15
β-strand	46-52	7	15
β-strand	57-60	4	15
α-helix	62-64	3
β-strand	68-73	6	14
α-helix	74-76	3
β-strand	78-83	6	14
α-helix	88-90	3
β-strand	92-99	8	15
β-strand	107-108	2	15
β-strand	112-116	5	15
β-strand	122	1	16
α-helix	123-124	2
β-strand	125-129	5	17
β-strand	138	1	17
β-strand	140-150	11	17
β-strand	151	1	16
β-strand	156-159	4	18
α-helix	160-162	3
β-strand	164	1	18
β-strand	168-170	3	17
α-helix	171-173	3
β-strand	174-175	2	17
β-strand	181-190	10	17
α-helix	192-194	3
β-strand	199-205	7	18
β-strand	210-216	7	18

Chain E: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
β-strand	10-13	4	20
β-strand	19-25	7	19
β-strand	30	1	21
β-strand	36	1	21
β-strand	38-43	6	20
α-helix	48-49	2
β-strand	50-54	5	20
β-strand	58-59	2	20
α-helix	60	1
β-strand	67-72	6	19
β-strand	75-80	6	19
α-helix	85-87	3
β-strand	89-95	7	20
β-strand	99	1	22
β-strand	102-103	2	20
β-strand	107-111	5	20
β-strand	116	1	23
β-strand	119-123	5	24
α-helix	124-126	3
α-helix	127-130	4
β-strand	134-144	11	24
β-strand	145	1	23
β-strand	149-155	7	25
β-strand	158-159	2	25
α-helix	160	1
β-strand	166-168	3	24
α-helix	169-172	4
β-strand	178-187	10	24
α-helix	188-192	5
β-strand	196-203	8	25
β-strand	210-211	2	25
β-strand	214-215	2	25

Chain F: 0 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	19-24	6	26
β-strand	29-34	6	26
β-strand	38-39	2	27
β-strand	45-46	2	27
β-strand	47	1	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epiregulin Antibody LY3016859 Fab Heavy Chain	A, D	protein	217	Homo sapiens
Epiregulin Antibody LY3016859 Fab Light Chain	B, E	protein	216	Homo sapiens
Protransforming growth factor alpha	C, F	protein	40	Homo sapiens	P01135 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>5KN5_1 Epiregulin Antibody LY3016859 Fab Heavy Chain (chains A, D)
QVQLVQSGAEVKKPGSSVKVSCKASGYTFTDAYINWVRQAPGQGLEWMGWIWPGPVITYY
NPKFKGRVTITADKSTSTAYMELSSLRSEDTAVYYCARREVLSPFAYWGQGTTVTVSSAS
TKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGL
YSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVE

Sequence of entity 2 (B, E), FASTA

>5KN5_2 Epiregulin Antibody LY3016859 Fab Light Chain (chains B, E)
DIVMTQSPDSLAVSLGERATINCRSSQSIVHSTGNTYLEWYQQKPGQPPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLTISSLQAEDVAVYYCFHGTHVPYTFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR

Sequence of entity 3 (C, F), FASTA

>5KN5_3 Protransforming growth factor alpha (chains C, F)
DSHTQFCFHGTCRFLVQEDKPACVCHSGYVGARCEHADLL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1

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

Primary citation

Structural basis of selectivity and neutralizing activity of a TGF alpha /epiregulin specific antibody. Boyles, J.S., Atwell, S., Druzina, Z. et al. Protein Sci (2016) 25:2028-2036. DOI 10.1002/pro.3023 · PubMed

Other PDB entries of the same protein (UniProt P01135 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3E50 2.3 Å, Crystal structure of human insulin degrading enzyme in complex with transforming growth…
1MOX 2.5 Å, Crystal Structure of Human Epidermal Growth Factor Receptor (residues 1-501) in complex…
7SZ7 3.4 Å, Cryo-EM structure of the extracellular module of the full-length EGFR bound to…
7SZ5 3.6 Å, Cryo-EM structure of the extracellular module of the full-length EGFR bound to TGF-alpha…
1GK5 Solution Structure the mEGF/TGFalpha44-50 chimeric growth factor
1YUF Type alpha transforming growth factor, NMR, 16 models without energy minimization
1YUG Type alpha transforming growth factor, NMR, 15 models after ECEPP/3 energy minimization
2TGF The solution structure of human transforming growth factor alpha
3TGF The solution structure of human transforming growth factor alpha
4TGF Solution structures of human transforming growth factor alpha derived from 1*H NMR data

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