4NJA: Fab 6C8

Crystal structure of Fab 6C8 in complex with MPTS. Determined by X-ray diffraction at 2.2 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,519
Mol. weight: 49.63 kDa
Ligands: PO4, 2M9, ZN
Released: 12 Nov 2014

Explore 4NJA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NJA contains 18 α-helices and 44 β-strands across 2 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: 10 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
α-helix	7	1
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-40	7	8
β-strand	44-51	8	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
β-strand	77-82	6	7
α-helix	84-86	3
β-strand	88-95	8	8
α-helix	100B-100C	2
β-strand	100D-103	4	8
β-strand	107-111	5	8
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
β-strand	137-147	11	10
β-strand	148	1	9
β-strand	153-157	4	11
α-helix	162-164	3
β-strand	166	1	11
β-strand	172-179	8	10
β-strand	184-194	11	10
α-helix	195-198	3
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11

Chain L: 8 helices, 23 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	27C-27D	2	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
α-helix	80-82	3
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	4
α-helix	112-113	2
β-strand	114-118	5	5
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	145-150	6	6
β-strand	153-154	2	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-188	6
β-strand	191-197	7	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
6C8 light chain	L	protein	218	Mus musculus	P01660 (AlphaFold model), Q52L95 (AlphaFold model)
6C8 heavy chain	H	protein	233	Mus musculus	A0A0F7R1P3 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4NJA_1 6C8 light chain (chains L)
DIVLTQSPASLAVSLGQRATISCRASESVDSYGNSFMHWYQQKPGQPPKLLIYRASNLES
GIPARFSGSGSRTDFTLTINPVEADDVATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>4NJA_2 6C8 heavy chain (chains H)
EVQLQQSGPELVKPGASVKMSCKASGYTFTDYYMHWVKQSHGKSLEWIGYIYPNNGGNGY
NQKFKGKATLTVDKSSSTAYMELRSLTSDDSAVYYCARRGGYGIRGYFDVWGTGTTVTVS
SAKTTPPSVYPLAPGCGDTTGSSVTSGCLVKGYFPEPVTVTWNSGSLSSSVHTFPALLQS
GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEPSGPISTINPCPPC

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	1
2M9	8-methoxypyrene-1,3,6-trisulfonic acid	C17 H12 O10 S3	1
ZN	Zinc ion	Zn	2

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

Primary citation

Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation. Adhikary, R., Yu, W., Oda, M. et al. Biochemistry (2015) 54:2085-2093. DOI 10.1021/bi501417q · PubMed

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

1J05 1.5 Å, The crystal structure of anti-carcinoembryonic antigen monoclonal antibody T84.66 Fv…
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
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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