6AYN: Cetuximab Fab light chain

Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant. Determined by X-ray diffraction at 2.48 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 2.48 Å
Organisms: Mus musculus, Homo sapiens, synthetic construct
Chains: 6
Atoms: 7,274
Mol. weight: 96.93 kDa
Released: 13 Dec 2017

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

Secondary structure: helices and β-sheets

6AYN contains 35 α-helices and 92 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: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-13	4	2
β-strand	19-25	7	1
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
β-strand	62-67	6	1
β-strand	70-75	6	1
α-helix	80-82	3
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	145-150	6	5
β-strand	153-154	2	5
α-helix	155	1
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18-25	8	6
β-strand	34-40	7	7
β-strand	44-51	8	7
β-strand	57-59	3	7
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	87-89	3
β-strand	91-98	8	7
β-strand	106-109	4	7
β-strand	113-117	5	7
β-strand	123	1	8
α-helix	124-125	2
β-strand	126-130	5	9
α-helix	134-136	3
β-strand	137-138	2	9
β-strand	141-151	11	9
β-strand	152	1	8
β-strand	157-160	4	10
α-helix	161-163	3
β-strand	165	1	10
β-strand	169-171	3	9
α-helix	172-174	3
β-strand	175-176	2	9
β-strand	182-191	10	9
α-helix	192-194	3
β-strand	201-206	6	10
α-helix	207-209	3
β-strand	211-216	6	10

Chain C: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
α-helix	42-44	3
β-strand	45-49	5	12
β-strand	53-54	2	12
β-strand	62-67	6	11
β-strand	70-75	6	11
α-helix	80-82	3
β-strand	84-90	7	12
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-106	5	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-154	2	15
α-helix	155	1
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-187	5
β-strand	191-197	7	15
β-strand	205-210	6	15

Chain D: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	16
α-helix	7-9	3
β-strand	10-12	3	17
β-strand	18-25	8	16
β-strand	34-40	7	17
β-strand	44-51	8	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	87-89	3
β-strand	91-98	8	17
β-strand	106-109	4	17
β-strand	113-117	5	17
β-strand	123	1	18
α-helix	124-125	2
β-strand	126-130	5	19
α-helix	134-136	3
β-strand	137-138	2	19
β-strand	141-151	11	19
β-strand	152	1	18
β-strand	157-160	4	20
α-helix	161-163	3
β-strand	165	1	20
β-strand	169-171	3	19
α-helix	172-174	3
β-strand	175-176	2	19
β-strand	182-191	10	19
α-helix	192-194	3
β-strand	200-206	7	20
α-helix	207-209	3
β-strand	211-217	7	20

Chains E and F: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	21
β-strand	9-10	2	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cetuximab Fab light chain	A, C	protein	213	Mus musculus, Homo sapiens	P01834 (AlphaFold model)
Cetuximab Fab heavy chain	B, D	protein	221	Mus musculus, Homo sapiens	S6B291 (AlphaFold model)
Cyclic meditope	E, F	protein	11	synthetic construct

Sequence of entity 1 (A, C), FASTA

>6AYN_1 Cetuximab Fab light chain (chains A, C)
DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYASESISGIPS
RFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGA

Sequence of entity 2 (B, D), FASTA

>6AYN_2 Cetuximab Fab heavy chain (chains B, D)
QVQLKQSGPGLVQPSQSLSITCTVSGFSLTNYGVHWVRQSPGKGLEWLGVIWSGGNTDYN
TPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKS

Sequence of entity 3 (E, F), FASTA

>6AYN_3 Cyclic meditope (chains E, F)
XQFDLSTXRLK

Primary citation

Meditope-Fab interaction: threading the hole. Bzymek, K.P., Ma, Y., Avery, K.N. et al. Acta Crystallogr F Struct Biol Commun (2017) 73:688-694. DOI 10.1107/S2053230X17016272 · PubMed

Other PDB entries of the same protein (UniProt P01834 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5EWI 1.6 Å, Crystal Structure of the Human Fab VRC38.01, an HIV-1 V1V2-Directed Neutralizing…
1NGZ 1.6 Å, Chimeric Germline Fab 7g12-apo
6N35 1.75 Å, Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement
4XMP 1.78 Å, Crystal structure of broadly and potently neutralizing antibody VRC08 in complex with…
1N0X 1.8 Å, Crystal Structure of a Broadly Neutralizing Anti-HIV-1 Antibody in Complex with a…
3VH8 1.8 Å, KIR3DL1 in complex with HLA-B*5701
3X12 1.8 Å, Crystal structure of HLA-B*57:01.I80N
6B9Z 1.82 Å, Trastuzumab Fab v3
2VXQ 1.9 Å, Crystal structure of the major grass pollen allergen Phl p 2 in complex with its…
3D85 1.9 Å, Crystal structure of IL-23 in complex with neutralizing FAB
6BAH 1.9 Å, Trastuzumab Fab v3 with 5-diphenyl meditope variant
6DCV 1.9 Å, Crystal structure of human anti-tau antibody CBTAU-27.1

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