6ARP: Mutant Cetuximab Fab fragment

Structure of a mutant Cetuximab Fab fragment. Determined by X-ray diffraction at 1.7 Å resolution. Released 29 Aug 2018.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,641
Mol. weight: 95.7 kDa
Released: 29 Aug 2018

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

Secondary structure: helices and β-sheets

6ARP contains 33 α-helices and 86 β-strands across 4 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	11
β-strand	10-13	4	12
β-strand	19-25	7	11
β-strand	33-38	6	12
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

Chains B and D: 9 helices, 22 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	34-39	6	17
β-strand	45-51	7	17
β-strand	57-59	3	17
α-helix	61-63	3
β-strand	67-72	6	16
α-helix	73-75	3
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
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	201-206	6	20
α-helix	207-209	3
β-strand	211-216	6	20

Chain C: 7 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	153-155	3	5
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cetuximab mutant light chain,Uncharacterized protein	A, C	protein	214	Homo sapiens	Q8TCD0 (AlphaFold model)
Cetuximab mutant Fab heavy chain,Immunoglobulin gamma-1 heavy chain	B, D	protein	222	Homo sapiens	P0DOX5 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>6ARP_1 Cetuximab mutant light chain,Uncharacterized protein (chains A, C)
DILLTQSPVILSVSPGERVSFSCRASQSIGTNIHWYQQRTNGSPRLLIKYADESIDGIPS
RFSGSGSGTDFTLSINSVESEDIADYYCQQNNNWPTTFGAGTKLELKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, D), FASTA

>6ARP_2 Cetuximab mutant Fab heavy chain,Immunoglobulin gamma-1 heavy chain (chains B, D)
QVQLKQSGPGLVQPSQSLSITCTVSGFDLTDYGVHWVRQSPGKGLEWLGVIWSGGNTDYN
TPFTSRLSINKDNSKSQVFFKMNSLQSNDTAIYYCARALTYYDYEFAYWGQGTLVTVSAA
STKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSG
LYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSC

Primary citation

Structure of a mutant Cetuximab Fab fragment. Christie, M., Christ, D. To be published.

Other PDB entries of the same protein (UniProt Q8TCD0 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4NWU 1.6 Å, Crystal structure of APE1551, an anti-human NGF Fab with a nine amino acid insertion in…
6DC4 1.7 Å, RSV-neutralizing human antibody AM22
4NWT 1.75 Å, Crystal structure of the anti-human NGF Fab APE1531
6UC5 1.75 Å, Fab397 in complex with NPNA peptide
3MNZ 1.8 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
4NUJ 1.83 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT152
4NUG 1.86 Å, Crystal structure of HIV-1 broadly neutralizing antibody PGT151
5VKK 2.01 Å, Crystal structure of Fab fragment of anti-CD22 Epratuzumab
3PGF 2.1 Å, Crystal structure of maltose bound MBP with a conformationally specific synthetic…
3MNW 2.2 Å, Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41…
6E4X 2.25 Å, Human antibody S5V2-29 in complex with influenza hemagglutinin A/Texas/50/2012 (H3N2)
4D9Q 2.28 Å, Inhibiting Alternative Pathway Complement Activation by Targeting the Exosite on Factor D

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