2OR9: Monoclonal anti-c-myc antibody 9E10

The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops. Determined by X-ray diffraction at 2.7 Å resolution. Released 12 Feb 2008.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Mus musculus
Chains: 5
Atoms: 7,182
Mol. weight: 99.12 kDa
Released: 12 Feb 2008

Explore 2OR9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2OR9 contains 29 α-helices and 96 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 H: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	8
β-strand	10-12	3	4
β-strand	16-25	10	8
α-helix	29-31	3
β-strand	34-39	6	4
β-strand	45-51	7	4
β-strand	57-58	2	4
β-strand	64	1	8
β-strand	67-72	6	8
β-strand	77-82C	9	8
α-helix	84-86	3
β-strand	88-100	13	4
β-strand	100C-103	11	4
β-strand	107-111	5	4
α-helix	115-116	2
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	153-154	2	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	175-184	10	10
β-strand	194-196	3	11
α-helix	200-202	3
β-strand	207-209	3	11

Chain I: 8 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	18
β-strand	10-12	3	19
β-strand	18-25	8	18
α-helix	29-31	3
β-strand	33-39	7	19
β-strand	45-51	7	19
β-strand	57-58	2	19
β-strand	64	1	18
β-strand	67-72	6	18
α-helix	73-75	3
β-strand	77-82	6	18
α-helix	84-86	3
β-strand	88-95	8	19
β-strand	96-100A	6	20
β-strand	100D-100I	6	20
β-strand	103	1	19
β-strand	107-111	5	19
α-helix	115-116	2
β-strand	117	1	21
α-helix	118-119	2
β-strand	120-124	5	22
β-strand	135-145	11	22
β-strand	146	1	21
β-strand	153-154	2	23
α-helix	155-157	3
β-strand	159	1	23
β-strand	163-165	3	22
α-helix	166-168	3
β-strand	169-170	2	22
β-strand	175-184	10	22
β-strand	194-199	6	23
α-helix	200-202	3
β-strand	204-209	6	23

Chain L: 7 helices, 24 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	27C-28	3	3
β-strand	30-31	2	3
β-strand	33-38	6	2
β-strand	45-49	5	2
β-strand	53-54	2	2
α-helix	55	1
β-strand	62-67	6	1
β-strand	70-75	6	1
β-strand	84-90	7	2
β-strand	97	1	4
β-strand	98	1	2
α-helix	99	1
β-strand	102-106	5	2
β-strand	111	1	5
β-strand	114-118	5	6
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	6
β-strand	140	1	5
β-strand	144-150	7	7
β-strand	153-155	3	7
β-strand	159-163	5	6
α-helix	164-167	4
β-strand	173-182	10	6
α-helix	183-188	6
β-strand	191-198	8	7
α-helix	204	1
β-strand	205-210	6	7

Chain M: 7 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	12
β-strand	10-14	5	13
β-strand	19-25	7	12
β-strand	27C-27D	2	14
β-strand	30-31	2	14
β-strand	33-38	6	13
β-strand	45-49	5	13
β-strand	53-54	2	13
α-helix	55	1
β-strand	62-67	6	12
β-strand	70-75	6	12
β-strand	84-90	7	13
α-helix	96	1
β-strand	97-98	2	13
β-strand	102-107	6	13
β-strand	111	1	15
β-strand	114-118	5	16
α-helix	119-121	3
α-helix	122-125	4
β-strand	129-139	11	16
β-strand	140	1	15
β-strand	144-150	7	17
β-strand	153-154	2	17
β-strand	159-163	5	16
α-helix	164-167	4
β-strand	173-182	10	16
α-helix	183-187	5
β-strand	191-198	8	17
α-helix	204	1
β-strand	205-210	6	17

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	2-5	4	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Monoclonal anti-c-myc antibody 9E10	L, M	protein	218	Mus musculus	P01654 (AlphaFold model)
Monoclonal anti-c-myc antibody 9E10	H, I	protein	228	Mus musculus
synthetic epitope peptide of 9E10	P	protein	11		P01106 (AlphaFold model)

Sequence of entity 1 (L, M), FASTA

>2OR9_1 Monoclonal anti-c-myc antibody 9E10 (chains L, M)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGFSFMNWFQQKPGQPPKLLIYAISNRGS
GVPARFSGSGSGTDFSLNIHPVEEDDPAMYFCQQTKEVPWTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H, I), FASTA

>2OR9_2 Monoclonal anti-c-myc antibody 9E10 (chains H, I)
EVHLVESGGDLVKPGGSLKLSCAASGFTFSHYGMSWVRQTPDKRLEWVATIGSRGTYTHY
PDSVKGRFTISRDNDKNALYLQMNSLKSEDTAMYYCARRSEFYYYGNTYYYSAMDYWGQG
ASVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTF
PAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

Sequence of entity 3 (P), FASTA

>2OR9_3 synthetic epitope peptide of 9E10 (chains P)
EQKLISEEDLN

Primary citation

The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops. Krauss, N., Wessner, H., Welfle, K. et al. Proteins (2008) 73:552-565. DOI 10.1002/prot.22080 · PubMed

Other PDB entries of the same protein (UniProt P01654 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2ORB 2.2 Å, The structure of the anti-c-myc antibody 9E10 Fab fragment
1MF2 2.6 Å, Anti HIV1 protease FAB complex

Browse structure collections

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