1NBV: IGG2B-kappa BV04-01 FAB

An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded FAB and a deoxynucleotide-FAB complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 31 Jan 1994.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Mus musculus
Chains: 2
Atoms: 3,347
Mol. weight: 47.66 kDa
Released: 31 Jan 1994

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

Secondary structure: helices and β-sheets

1NBV contains 11 α-helices and 42 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: 3 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	6
β-strand	11-12	2	7
β-strand	17-23	7	6
β-strand	34-39	6	8
β-strand	46-51	6	8
α-helix	54-56	3
β-strand	60-62	3	8
α-helix	64-66	3
β-strand	67	1	6
β-strand	70-74	5	6
β-strand	80-86	7	6
β-strand	94-100	7	8
β-strand	110-111	2	8
β-strand	115-117	3	8
β-strand	118-119	2	7
β-strand	125	1	9
β-strand	128-132	5	10
β-strand	143-153	11	10
β-strand	154	1	9
β-strand	159-163	5	11
β-strand	172-179	8	10
β-strand	182-192	11	10
β-strand	201-207	7	11
α-helix	208-210	3
β-strand	212-218	7	11

Chain L: 8 helices, 20 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	38-43	6	2
α-helix	48	1
β-strand	49-54	6	2
β-strand	58-59	2	2
α-helix	60	1
β-strand	67-72	6	1
β-strand	75-80	6	1
β-strand	90-95	6	2
α-helix	101	1
β-strand	102-103	2	2
β-strand	107-111	5	2
β-strand	116	1	3
β-strand	119-123	5	4
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	4
β-strand	145	1	3
β-strand	150-155	6	5
β-strand	164-168	5	4
α-helix	169-172	4
β-strand	178-187	10	4
α-helix	188-191	4
β-strand	196-202	7	5
β-strand	210-215	6	5
α-helix	216-218	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
IGG2B-kappa BV04-01 FAB (light chain)	L	protein	219	Mus musculus	A2NHM3 (AlphaFold model)
IGG2B-kappa BV04-01 FAB (heavy chain)	H	protein	219	Mus musculus	P01867 (AlphaFold model)

Sequence of entity 1 (L), FASTA

>1NBV_1 IGG2B-KAPPA BV04-01 FAB (LIGHT CHAIN) (chains L)
DVVMTQTPLSLPVSLGDQASISCRSSQSLVHSNGNTYLHWYLQKPGQSPKLLIYKVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDLGVYFCSQSTHVPLTFGAGTKLELKRADAAPTV
SIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSM
SSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 2 (H), FASTA

>1NBV_2 IGG2B-KAPPA BV04-01 FAB (HEAVY CHAIN) (chains H)
EVQPVETGGGLVQPKGSLKLSCAASGFSFNTNAMNWVRQAPGKGLEWVARIRSKSNNYAT
YYADSVKDRFTISRDDSQNMLYLQMNNLKTEDTAMYYCVRDQTGTAWFAYWGQGTLVTVS
AAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPALLQS
GLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLE

Primary citation

An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex. Herron, J.N., He, X.M., Ballard, D.W. et al. Proteins (1991) 11:159-175. DOI 10.1002/prot.340110302 · PubMed

Other PDB entries of the same protein (UniProt A2NHM3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6PXR 1.56 Å, Anti-TAU BIIB092 FAB with TAU peptide
4TPR 1.6 Å, Structure of Tau5 antibody Fab fragment
4TQE 1.6 Å, Structure of tau peptide in complex with Tau5 antibody Fab fragment
3V4U 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
3UO1 1.64 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2IPU 1.65 Å, PFA1 Fab fragment complexed with Abeta 1-8 peptide
3V52 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
2DQU 1.7 Å, Crystal form II: high resolution crystal structure of the complex of the hydrolytic…
3UYR 1.7 Å, Structure of a monoclonal antibody complexed with its MHC-I antigen
1ZEA 1.78 Å, Structure of the anti-cholera toxin antibody Fab fragment TE33 in complex with a D-peptide
1PZ5 1.8 Å, Structural basis of peptide-carbohydrate mimicry in an antibody combining site
2DQT 1.8 Å, High resolution crystal structure of the complex of the hydrolytic antibody Fab 6D9 and…

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