1YY9: Epidermal Growth Factor Receptor

Structure of the extracellular domain of the epidermal growth factor receptor in complex with the Fab fragment of cetuximab/Erbitux/IMC-C225. Determined by X-ray diffraction at 2.6 Å resolution. Released 26 Apr 2005.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Homo sapiens, Mus musculus
Chains: 3
Atoms: 8,225
Mol. weight: 120.24 kDa
Ligands: NAG
Released: 26 Apr 2005

Explore 1YY9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1YY9 contains 42 α-helices and 119 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: 29 helices, 72 β-strands

Element	Residues	Length	Sheet
β-strand	6-7	2	1
α-helix	20-31	12
β-strand	36-37	2	1
β-strand	41-44	4	2
α-helix	46-47	2
α-helix	53-57	5
β-strand	60-61	2	1
β-strand	65-68	4	2
β-strand	74	1	3
β-strand	82-83	2	1
β-strand	93-98	6	2
β-strand	101	1	4
β-strand	107	1	4
β-strand	110	1	3
β-strand	118-119	2	1
β-strand	123-127	5	2
α-helix	135-137	3
α-helix	140-142	3
β-strand	144	1	1
α-helix	149-151	3
β-strand	153-154	2	2
α-helix	171-173	3
β-strand	175	1	5
α-helix	180-182	3
β-strand	183	1	5
β-strand	199	1	6
α-helix	204-206	3
β-strand	207	1	6
α-helix	208-209	2
β-strand	212	1	7
β-strand	216	1	8
β-strand	224	1	8
β-strand	227	1	7
β-strand	230-231	2	9
β-strand	236-237	2	9
α-helix	240-242	3
β-strand	244-247	4	10
β-strand	252-255	4	10
β-strand	261-263	3	9
β-strand	266-268	3	9
α-helix	271-272	2
β-strand	276-277	2	11
β-strand	282	1	9
β-strand	283-284	2	11
α-helix	287-288	2
β-strand	291-295	5	11
β-strand	300-304	5	11
α-helix	309-310	2
β-strand	312-314	3	12
β-strand	317	1	13
α-helix	319-321	3
β-strand	322	1	13
α-helix	332-335	4
β-strand	340-342	3	12
β-strand	345-347	3	14
α-helix	349-353	5
β-strand	355	1	15
α-helix	356-358	3
β-strand	360	1	15
α-helix	361-363	3
α-helix	365-373	9
β-strand	376-377	2	12
β-strand	381-383	3	14
α-helix	394-396	3
β-strand	401-402	2	12
β-strand	408	1	14
β-strand	412-417	6	14
β-strand	431-432	2	12
β-strand	436-440	5	14
α-helix	453-455	3
β-strand	457	1	12
β-strand	464-467	4	14
β-strand	469	1	16
α-helix	472-477	6
β-strand	486	1	17
β-strand	491	1	18
α-helix	496-498	3
β-strand	499	1	18
β-strand	502	1	17
β-strand	505-506	2	19
β-strand	511-512	2	19
β-strand	524-527	4	19
β-strand	530-533	4	19
α-helix	534-535	2
β-strand	538	1	20
α-helix	539-541	3
β-strand	547	1	21
β-strand	555	1	21
β-strand	558	1	20
β-strand	561-563	3	22
β-strand	566-568	3	22
β-strand	573-575	3	23
α-helix	578-580	3
β-strand	583-584	2	23
β-strand	585-587	3	24
β-strand	592	1	22
β-strand	593-595	3	24
α-helix	596-597	2
β-strand	601	1	25
β-strand	603	1	25
α-helix	609-611	3

Chain C: 5 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-13	4	27
β-strand	19-25	7	26
β-strand	33-38	6	27
β-strand	45-49	5	27
β-strand	53-54	2	27
β-strand	62-66	5	26
β-strand	70-75	6	26
β-strand	85-90	6	27
β-strand	93	1	16
α-helix	96	1
β-strand	97-98	2	27
β-strand	102-106	5	27
β-strand	111	1	28
α-helix	112-113	2
β-strand	114-118	5	29
α-helix	119-121	3
β-strand	129-139	11	29
β-strand	140	1	28
β-strand	145-150	6	30
β-strand	153-154	2	30
α-helix	155	1
β-strand	159-163	5	29
α-helix	164-167	4
β-strand	173-182	10	29
β-strand	183	1	31
β-strand	186	1	31
β-strand	189	1	31
β-strand	192-197	6	30
β-strand	205-207	3	30

Chain D: 8 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	32
β-strand	11-12	2	33
α-helix	17	1
β-strand	18-25	8	32
β-strand	34-40	7	34
β-strand	44-51	8	34
β-strand	57-59	3	34
α-helix	61-63	3
β-strand	67-72	6	32
α-helix	73-75	3
β-strand	77-82	6	32
α-helix	87-89	3
β-strand	91-98	8	34
β-strand	106-109	4	34
β-strand	113-115	3	34
β-strand	116-117	2	33
α-helix	120-122	3
β-strand	123	1	35
β-strand	126-130	5	36
α-helix	131-133	3
β-strand	142-151	10	36
β-strand	152	1	35
β-strand	157-160	4	37
α-helix	161-163	3
β-strand	169-171	3	36
α-helix	172-174	3
β-strand	175-176	2	36
β-strand	182-190	9	36
β-strand	201-206	6	37
β-strand	211-216	6	37

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Epidermal Growth Factor Receptor	A	protein	624	Homo sapiens	P00533 (AlphaFold model)
Cetuximab Fab Light chain	C	protein	213	Mus musculus, Homo sapiens
Cetuximab Fab Heavy chain	D	protein	221	Mus musculus, Homo sapiens

Sequence of entity 1 (A), FASTA

>1YY9_1 Epidermal Growth Factor Receptor (chains A)
LEEKKVCQGTSNKLTQLGTFEDHFLSLQRMFNNCEVVLGNLEITYVQRNYDLSFLKTIQE
VAGYVLIALNTVERIPLENLQIIRGNMYYENSYALAVLSNYDANKTGLKELPMRNLQEIL
HGAVRFSNNPALCNVESIQWRDIVSSDFLSNMSMDFQNHLGSCQKCDPSCPNGSCWGAGE
ENCQKLTKIICAQQCSGRCRGKSPSDCCHNQCAAGCTGPRESDCLVCRKFRDEATCKDTC
PPLMLYNPTTYQMDVNPEGKYSFGATCVKKCPRNYVVTDHGSCVRACGADSYEMEEDGVR
KCKKCEGPCRKVCNGIGIGEFKDSLSINATNIKHFKNCTSISGDLHILPVAFRGDSFTHT
PPLDPQELDILKTVKEITGFLLIQAWPENRTDLHAFENLEIIRGRTKQHGQFSLAVVSLN
ITSLGLRSLKEISDGDVIISGNKNLCYANTINWKKLFGTSGQKTKIISNRGENKCKATGQ
VCHALCSPEGCWGPEPRDCVSCRNVSRGRECVDKCKLLEGEPREFVENSECIQCHPECLP
QAMNITCTGRGPDNCIQCAHYIDGPHCVKTCPAGVMGENNTLVWKYADAGHVCHLCHPNC
TYGCTGPGLRGCPTNGPKHHHHHH

Sequence of entity 2 (C), FASTA

>1YY9_2 Cetuximab Fab Light chain (chains C)
DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPS
RFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA

Sequence of entity 3 (D), FASTA

>1YY9_3 Cetuximab Fab Heavy chain (chains D)
QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYN
TPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS

Ligands and cofactors

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

Primary citation

Structural basis for inhibition of the epidermal growth factor receptor by cetuximab. Li, S., Schmitz, K.R., Jeffrey, P.D. et al. Cancer Cell (2005) 7:301-311. DOI 10.1016/j.ccr.2005.03.003 · PubMed

Other PDB entries of the same protein (UniProt P00533 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8A27 1.07 Å, EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2…
8A2D 1.11 Å, EGFR kinase domain (L858R/V948R) in complex with 2-[4-(difluoromethyl)-6-[2-[4-[[4-(hydro…
5UG9 1.33 Å, Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a…
5HG8 1.42 Å, EGFR (L858R, T790M, V948R) in complex with N-[3-({2-[(1-methyl-1H-pyrazol-4-yl)amino]-7H-…
8A2A 1.43 Å, EGFR kinase domain in complex with 2-(6,7-dihydro-5H-pyrrolo[1,2-c]imidazol-1-yl)-2-[6-[2…
5UG8 1.46 Å, Crystal structure of the EGFR kinase domain (L858R, T790M, V948R) in complex with a…
3POZ 1.5 Å, EGFR Kinase domain complexed with tak-285
6TFV 1.5 Å, Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 18b
6TG0 1.5 Å, Crystal Structure of EGFR T790M/V948R in Complex with Covalent Pyrrolopyrimidine 21a
3VRP 1.52 Å, Crystal structure of the tyrosine kinase binding domain of Cbl-c in complex with…
5HG5 1.52 Å, EGFR (L858R, T790M, V948R) in complex with N-{3-[(2-{[4-(4-methylpiperazin-1-yl)phenyl]am…
5CNO 1.55 Å, Crystal structure of the EGFR kinase domain mutant V924R

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1YY9 is part of these collections:

Antibodies and the immune system

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