1J05: Anti-CEA mAb T84.66, light chain

The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment. Determined by X-ray diffraction at 1.5 Å resolution. Released 16 Dec 2003.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Mus musculus
Chains: 4
Atoms: 3,859
Mol. weight: 51.07 kDa
Ligands: PO4
Released: 16 Dec 2003

Explore 1J05 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1J05 contains 16 α-helices and 51 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: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-12	3	8
β-strand	19-25	7	7
β-strand	27C	1	9
β-strand	31	1	9
β-strand	33-38	6	8
β-strand	45-49	5	8
β-strand	53-54	2	8
α-helix	55	1
β-strand	62-65	4	7
β-strand	70-75	6	7
α-helix	80-82	3
β-strand	84-90	7	8
α-helix	96	1
β-strand	97-98	2	8
β-strand	102-105	4	8

Chain B: 5 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	10
α-helix	7-9	3
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	46-52	7	11
β-strand	56-59	4	11
α-helix	61-63	3
β-strand	67-72	6	10
α-helix	73-75	3
β-strand	77-82	6	10
α-helix	84-86	3
β-strand	88-95	8	11
β-strand	96	1	12
β-strand	100	1	12
β-strand	107-111	5	11

Chain H: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	4
α-helix	7-9	3
β-strand	10-12	3	5
β-strand	18-25	8	4
α-helix	29-31	3
β-strand	33-39	7	5
β-strand	45-52	8	5
β-strand	56-59	4	5
α-helix	61-63	3
β-strand	64	1	4
β-strand	67-72	6	4
α-helix	73-75	3
β-strand	77-82	6	4
α-helix	84-86	3
β-strand	88-95	8	5
β-strand	96	1	6
β-strand	100	1	6
β-strand	107-111	5	5

Chain L: 3 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-12	3	2
β-strand	19-25	7	1
β-strand	27C-27D	2	3
β-strand	30-31	2	3
β-strand	33-38	6	2
β-strand	44-49	6	2
β-strand	53-54	2	2
α-helix	55	1
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	102-105	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
anti-CEA mAb T84.66, light chain	A, L	protein	111	Mus musculus	P01660 (AlphaFold model)
anti-CEA mAb T84.66, heavy chain	B, H	protein	121	Mus musculus	Q9JL85 (AlphaFold model)

Sequence of entity 1 (A, L), FASTA

>1J05_1 anti-CEA mAb T84.66, light chain (chains A, L)
DIVLTQSPASLAVSLGQRATMSCRAGESVDIFGVGFLHWYQQKPGQPPKLLIYRASNLES
GIPVRFSGTGSRTDFTLIIDPVEADDVATYYCQQTNEDPYTFGGGTKLEIK

Sequence of entity 2 (B, H), FASTA

>1J05_2 anti-CEA mAb T84.66, heavy chain (chains B, H)
EVQLQQSGAELVEPGASVKLSCTASGFNIKDTYMHWVKQRPEQGLEWIGRIDPANGNSKY
VPKFQGKATITADTSSNTAYLQLTSLTSEDTAVYYCAPFGYYVSDYAMAYWGQGTSVTVS
S

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	2

Water and common crystallization additives (GOL) are not listed.

Primary citation

The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv fragment. Kondo, H., Nishimura, Y., Shiroishi, M. et al. To be published.

Other PDB entries of the same protein (UniProt P01660 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1I8K 1.8 Å, Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant…
2VL5 2.1 Å, Structure of anti-collagen type II FAb CIIC1
4NJA 2.2 Å, Crystal structure of Fab 6C8 in complex with MPTS
1EJO 2.3 Å, FAB fragment of neutralising monoclonal antibody 4C4 complexed with G-H loop from fmdv.
1I8I 2.4 Å, Crystal structure of dsfv MR1 in complex with the peptide antigen of the mutant…
1MOE 2.6 Å, The three-dimensional structure of an engineered scFv T84.66 dimer or diabody in VL to…
2R29 3.0 Å, Neutralization of dengue virus by a serotype cross-reactive antibody elucidated by…
3BSZ 3.38 Å, Crystal structure of the transthyretin-retinol binding protein-Fab complex
1QFW 3.5 Å, Ternary complex of human chorionic gonadotropin with fv anti alpha subunit and fv anti…
2R69 3.8 Å, Crystal structure of Fab 1A1D-2 complexed with E-DIII of Dengue virus at 3.8 angstrom…
2R6P 24.0 Å, Fit of E protein and Fab 1A1D-2 into 24 angstrom resolution cryoEM map of Fab complexed…

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