2ORB: Anti-c-myc antibody 9E10 Fab fragment

The structure of the anti-c-myc antibody 9E10 Fab fragment. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Feb 2008.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 4
Atoms: 6,731
Mol. weight: 97.99 kDa
Released: 12 Feb 2008

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

Secondary structure: helices and β-sheets

2ORB contains 27 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 H: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	10-12	3	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-39	6	7
β-strand	45-51	7	7
β-strand	57-58	2	7
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-95	8	7
α-helix	96	1
β-strand	100J-103	4	7
β-strand	107-111	5	7
α-helix	114-116	3
β-strand	117	1	8
β-strand	120-124	5	9
β-strand	135-145	11	9
β-strand	146	1	8
β-strand	151-154	4	10
α-helix	155-157	3
β-strand	159	1	10
β-strand	163-165	3	9
α-helix	166-168	3
β-strand	169-170	2	9
β-strand	175-184	10	9
β-strand	194-199	6	10
α-helix	200-202	3
β-strand	204-209	6	10

Chain I: 6 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	16
β-strand	10-12	3	17
β-strand	18-25	8	16
α-helix	29-31	3
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	57-58	2	17
β-strand	67-72	6	16
β-strand	77-82	6	16
α-helix	84-86	3
β-strand	88-94	7	17
β-strand	102-103	2	17
β-strand	107-111	5	17
α-helix	114-116	3
β-strand	117	1	18
β-strand	120-124	5	19
β-strand	135-145	11	19
β-strand	146	1	18
β-strand	151-154	4	20
α-helix	155-157	3
β-strand	159	1	20
β-strand	163-165	3	19
α-helix	166-168	3
β-strand	169-170	2	19
β-strand	175-184	10	19
β-strand	194-199	6	20
α-helix	200-202	3
β-strand	204-209	6	20

Chain L: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-14	5	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
α-helix	55	1
β-strand	62-66	5	1
β-strand	70-75	6	1
β-strand	84-90	7	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-107	6	2
β-strand	111	1	3
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	183-188	6
β-strand	191-197	7	5
β-strand	205-210	6	5

Chain M: 8 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	10-14	5	12
β-strand	19-25	7	11
β-strand	34-38	5	12
β-strand	45-49	5	12
β-strand	53-54	2	12
α-helix	55	1
β-strand	62-66	5	11
β-strand	70-75	6	11
β-strand	84-90	7	12
α-helix	94	1
α-helix	96	1
β-strand	97-98	2	12
β-strand	102-107	6	12
β-strand	111	1	13
α-helix	112-113	2
β-strand	114-118	5	14
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	14
β-strand	140	1	13
β-strand	145-150	6	15
β-strand	153-155	3	15
β-strand	159-163	5	14
α-helix	164-167	4
β-strand	173-182	10	14
α-helix	183-188	6
β-strand	191-197	7	15
β-strand	205-210	6	15

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

Sequence of entity 1 (L, M), FASTA

>2ORB_1 Monoclonal anti-c-myc antibody 9E10 (chains L, M)
DIVLTQSPASLAVSLGQRATISCRASESVDNYGFSFMNWFQQKPGQPPKLLIYAISNRGS
GVPARFSGSGSGTDFSLNIHPVEEDDPAMYFCQQTKEVPWTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H, I), FASTA

>2ORB_2 Monoclonal anti-c-myc antibody 9E10 (chains H, I)
EVHLVESGGDLVKPGGSLKLSCAASGFTFSHYGMSWVRQTPDKRLEWVATIGSRGTYTHY
PDSVKGRFTISRDNDKNALYLQMNSLKSEDTAMYYCARRSEFYYYGNTYYYSAMDYWGQG
ASVTVSSAKTTPPSVYPLAPGSAAQTNSMVTLGCLVKGYFPEPVTVTWNSGSLSSGVHTF
PAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD

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:

1MF2 2.6 Å, Anti HIV1 protease FAB complex
2OR9 2.7 Å, The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex…

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