4NJ9: Fab 8B10

Crystal structure of Fab 8B10 in complex with MPTS. Determined by X-ray diffraction at 1.95 Å resolution. Released 12 Nov 2014.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,581
Mol. weight: 49.47 kDa
Ligands: ZN, 2M9
Released: 12 Nov 2014

Explore 4NJ9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NJ9 contains 19 α-helices and 45 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	7
β-strand	10-12	3	8
β-strand	18-25	8	7
α-helix	29-31	3
β-strand	34-39	6	8
β-strand	45-51	7	8
β-strand	57-59	3	8
α-helix	61-63	3
β-strand	67-72	6	7
α-helix	73-75	3
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	171-173	3	10
α-helix	174-176	3
β-strand	177-179	3	10
β-strand	184-194	11	10
β-strand	206-212	6	11
α-helix	213-215	3
β-strand	217-222	6	11
α-helix	224-226	3

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	122-125	4
β-strand	129-139	11	5
β-strand	140	1	4
β-strand	146-150	5	6
β-strand	153-155	3	6
β-strand	159-163	5	5
α-helix	164-167	4
β-strand	173-182	10	5
α-helix	183-186	4
β-strand	191-196	6	6
β-strand	205-210	6	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
8B10 light chain	L	protein	218	Mus musculus	Q52L95 (AlphaFold model)
8B10 heavy chain	H	protein	229	Mus musculus	Q9D8L4 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>4NJ9_1 8B10 light chain (chains L)
DIVLTQSPASLAVSLGQRATISCRASESVDSYGISFMHWYQQKPGQPPKLLIYRASNLES
GIPARFSGSGSRTDFTLTIIPVEADDVATYYCQQSNEDPRTFGGGTKLEIKRADAAPTVS
IFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMS
STLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>4NJ9_2 8B10 heavy chain (chains H)
EVQLQQSGPELVKPGTSVKMSCKASGYTFTDYYMHWVKQSHGKSLEWIGYIYPNNGGNGY
NQKFKGKATLTVDKSSSTAYMELRSLTSEDSAVYYCARRGGYGSRGYFDVWGTGTTVTVS
SAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPALLQS
GLYTLSSSVTVTSNTWPSQTITCNVAHPASSTKVDKKIEPRGPISTINP

Ligands and cofactors

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

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 Q52L95 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3OZ9 1.6 Å, Crystal Structure of anti-gp41 Fab NC-1
4NJA 2.2 Å, Crystal structure of Fab 6C8 in complex with MPTS

Browse structure collections

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