1A6V: B1-8 FV fragment

B1-8 FV fragment complexed with a (4-hydroxy-3-nitrophenyl) acetate compound. Determined by X-ray diffraction at 1.8 Å resolution. Released 15 Jul 1998.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: Mus musculus
Chains: 6
Atoms: 5,798
Mol. weight: 76.15 kDa
Ligands: NPC
Released: 15 Jul 1998

Explore 1A6V in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1A6V contains 10 α-helices and 70 β-strands across 6 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: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	303-305	3	3
β-strand	309-311	3	4
β-strand	318-325	8	3
α-helix	329-331	3
β-strand	333-339	7	4
β-strand	346-351	6	4
β-strand	358-360	3	4
α-helix	362-364	3
β-strand	368-373	6	3
β-strand	378-383	6	3
β-strand	392-399	8	4
β-strand	410	1	4
β-strand	414-417	4	4

Chain I: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	303-305	3	8
β-strand	309-312	4	9
β-strand	318-325	8	8
β-strand	333-339	7	9
β-strand	345-351	7	9
β-strand	358-360	3	9
α-helix	362-364	3
β-strand	368-373	6	8
β-strand	378-383	6	8
α-helix	388-390	3
β-strand	392-399	8	9
β-strand	407-410	4	9
β-strand	414-418	5	9

Chain J: 1 helix, 13 β-strands

Element	Residues	Length	Sheet
β-strand	303-305	3	13
β-strand	309-311	3	14
β-strand	318-319	2	15
β-strand	322-325	4	13
β-strand	333-339	7	14
β-strand	345-350	6	14
β-strand	359-360	2	14
β-strand	372-373	2	13
β-strand	378-379	2	13
β-strand	382-383	2	15
α-helix	388-390	3
β-strand	392-399	8	14
β-strand	407-410	4	14
β-strand	414-417	4	14

Chain L: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	1
β-strand	9-11	3	2
β-strand	17-24	8	1
α-helix	31-33	3
β-strand	36-41	6	2
β-strand	45-51	7	2
β-strand	55-56	2	2
α-helix	57	1
β-strand	64-69	6	1
β-strand	72-78	7	1
α-helix	82-84	3
β-strand	86-94	9	2
β-strand	97-100	4	2
β-strand	104-107	4	2

Chain M: 2 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	5
β-strand	9-12	4	6
β-strand	18-22	5	7
β-strand	23	1	5
α-helix	31-33	3
β-strand	36-41	6	6
β-strand	45-51	7	6
β-strand	55-56	2	6
α-helix	57	1
β-strand	64-69	6	7
β-strand	72-77	6	7
β-strand	86-93	8	6
β-strand	98-100	3	6
β-strand	104-108	5	6

Chain N: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	5-6	2	10
β-strand	9-12	4	11
β-strand	18-23	6	10
β-strand	36-41	6	11
β-strand	45-50	6	11
β-strand	51	1	12
β-strand	55	1	12
β-strand	64-69	6	10
β-strand	72-77	6	10
β-strand	86-94	9	11
β-strand	97-100	4	11
β-strand	104-108	5	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
B1-8 fv (light chain)	L, M, N	protein	110	Mus musculus	P01724 (AlphaFold model)
B1-8 fv (heavy chain)	H, I, J	protein	120	Mus musculus	P01751

Sequence of entity 1 (L, M, N), FASTA

>1A6V_1 B1-8 FV (LIGHT CHAIN) (chains L, M, N)
QAVVTQESALTTSPGETVTLTCRSSTGAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGV
PARFSGSLIGNKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKLTVLE

Sequence of entity 2 (H, I, J), FASTA

>1A6V_2 B1-8 FV (HEAVY CHAIN) (chains H, I, J)
QVQLQQPGAELVKPGASVKLSCKASGYTFTSYWMHWVKQRPGRGLEWIGRIDPNSGGTKY
NEKFKSKATLTVDKPSSTAYMQLSSLTSEDSAVYYCARYDYYGSSYFDYWGQGTTVTVSS

Ligands and cofactors

ID	Name	Formula	Copies
NPC	4-hydroxy-3-nitrophenylacetyl-epsilon-aminocaproic acid anion	C14 H17 N2 O6	3

Primary citation

X-Ray Structures of Fv Fragment and its (4-Hydroxy-3-Nitrophenyl)Acetate Complex of Murine B1-8 Antibody. Simon, T., Henrick, K., Hirshberg, M. et al. To be published.

Other PDB entries of the same protein (UniProt P01724 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1OAQ 1.5 Å, Free conformation Ab1 of the IgE SPE-7
1OAU 1.8 Å, Fv Structure of the IgE SPE-7 in complex with DNP-Ser (immunising hapten)
1A6W 2.0 Å, B1-8 fv fragment complexed with a (4-hydroxy-5-iodo-3-nitrophenyl) acetate compound
1OCW 2.0 Å, Free conformation Ab2 of the IgE SPE-7
1Q0Y 2.0 Å, Anti-Morphine Antibody 9B1 Complexed with Morphine
1A6U 2.1 Å, B1-8 fv fragment
2BJM 2.15 Å, SPE7:Anthrone Complex
1OAR 2.23 Å, Fv IgE SPE-7 in complex with Alizarin Red
1DL7 2.35 Å, The structural basis of repertoire shift in an immune response to phosphocholine
1OAY 2.66 Å, Antibody multispecificity mediated by conformational diversity
1OAX 2.67 Å, Fv Structure of the IgE SPE-7 in complex with acenaphthenequinone
1OAZ 2.78 Å, IgE Fv SPE7 complexed with a recombinant thioredoxin

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