9FYS: D11 mAbs

Name: PDB 9FYS: D11 mAbs bound to alpha-Bungarotoxin
Published: 2025-07-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: toxin

D11 mAbs bound to alpha-Bungarotoxin. Determined by X-ray diffraction at 1.32 Å resolution. Released 16 Jul 2025.

Method: X-ray diffraction
Resolution: 1.32 Å
Organisms: Homo sapiens, Bungarus multicinctus
Chains: 6
Atoms: 5,926
Mol. weight: 77.31 kDa
Released: 16 Jul 2025

Explore 9FYS in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FYS contains 22 α-helices and 61 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 B: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-24	7	13
β-strand	34-39	6	14
β-strand	45-52	8	14
β-strand	57-60	4	14
β-strand	65	1	13
β-strand	68-73	6	13
α-helix	74-76	3
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-99	8	14
β-strand	104-105	2	5
β-strand	108-110	3	5
β-strand	118-121	4	14
β-strand	125-129	5	14

Chain C: 3 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	146-148	3
β-strand	150-151	2	1
β-strand	155-158	4	2
β-strand	164-170	7	1
α-helix	175-177	3
β-strand	181-185	5	2
β-strand	192-195	4	2
β-strand	196	1	3
β-strand	200	1	3
β-strand	209-214	6	1
β-strand	219-224	6	1
α-helix	229-231	3
β-strand	233-241	9	2
β-strand	246-249	4	2
β-strand	253-257	5	2

Chain I: 4 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
α-helix	7-9	3
β-strand	10-12	3	9
β-strand	18-25	8	8
β-strand	34-39	6	9
β-strand	45-52	8	9
β-strand	57-60	4	9
β-strand	68-73	6	8
α-helix	74-76	3
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	104-105	2	7
β-strand	108-110	3	7
β-strand	118-121	4	9
β-strand	125-129	5	9
α-helix	130	1

Chain M: 4 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	146-149	4
β-strand	150-151	2	10
β-strand	155-158	4	11
β-strand	164-170	7	10
α-helix	175-177	3
β-strand	181-185	5	11
β-strand	192-195	4	11
β-strand	196	1	12
β-strand	200	1	12
β-strand	209-214	6	10
α-helix	215-217	3
β-strand	219-224	6	10
α-helix	229-231	3
β-strand	233-241	9	11
β-strand	246-249	4	11
β-strand	253-257	5	11

Chain X: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	4
β-strand	12-15	4	4
α-helix	16-17	2
β-strand	22-28	7	5
α-helix	33-36	4
β-strand	39-45	7	5
α-helix	48-50	3
β-strand	56-60	5	5
α-helix	69-71	3

Chain Z: 4 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	6
β-strand	12-15	4	6
α-helix	16-17	2
β-strand	22-28	7	7
α-helix	33-36	4
β-strand	39-45	7	7
α-helix	48-52	5
β-strand	56-60	5	7
α-helix	69-71	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
heavy chain	C, M	protein	121	Homo sapiens
Alpha-bungarotoxin	X, Z	protein	95	Bungarus multicinctus	P60615 (AlphaFold model)
D11 mAbs Light chain	B, I	protein	144	Homo sapiens

Sequence of entity 1 (C, M), FASTA

>9FYS_1 heavy chain (chains C, M)
GASNFMLTQPRSVSESPGKTVTISCTRSSGSIGSDYVHWYQQRPGSSPTTVIYEDNQRPS
GVPDRFSGSIDSSSNSASLTISGLKTEDEADYYCQSYDRSNHEVVFGGGTKLTVLENLYF
Q

Sequence of entity 2 (X, Z), FASTA

>9FYS_2 Alpha-bungarotoxin (chains X, Z)
MKTLLLTLVVVTIVCLDLGYTIVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKV
VELGCAATCPSKKPYEEVTCCSTDKCNPHPKQRPG

Sequence of entity 3 (B, I), FASTA

>9FYS_3 D11 mAbs Light chain (chains B, I)
AQVQLVQSGAEVKKPGSSVKVSCKASGGTFSSYAISWVRQAPGQGLEWMGGIIPIFGTAN
YAQKFQGRVTITADESTSTAYMELRSLRSDDTAVYYCARDNLGYCSGGSCYSDYYYYYMD
VWGQGTLVTVSSGGGGSGGGGSGG

Primary citation

Rational design of antibodies with pH-dependent antigen-binding properties using structural insights from broadly neutralizing antibodies against alpha-neurotoxins. Wade, J., Strancar, N., Fernandez-Quintero, M.L. et al. MAbs (2025) 17:2553624-2553624. DOI 10.1080/19420862.2025.2553624 · PubMed

Other PDB entries of the same protein (UniProt P60615 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9HUB 1.33 Å, D11 mAbs bound to alpha-Bungarotoxin at pH 7.5
1HC9 1.8 Å, alpha-bungarotoxin complexed with high affinity peptide
8VY8 2.4 Å, Recombinant alpha bungarotoxin complexed with HAP peptide
9GU1 2.48 Å, Human adult muscle nAChR in resting state in nanodisc with alpha-bungarotoxin
2ABX 2.5 Å, The crystal structure of alpha-bungarotoxin at 2.5 Å resolution. Relation to solution…
8DA1 2.67 Å, Crystal structure of Krait alpha-neurotoxin in complex with Centi-LNX-D09 antibody
6UWZ 2.69 Å, Cryo-EM structure of Torpedo acetylcholine receptor in complex with alpha-bungarotoxin
9GU0 2.96 Å, Human adult muscle nAChR in resting state in detergent with alpha-bungarotoxin
1ABT NMR solution structure of an alpha-bungarotoxin(slash)nicotinic receptor peptide complex
1BXP Solution NMR structure of the complex of alpha-bungarotoxin with a library derived…
1HAA A beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungarotoxin with High…
1HAJ A beta-Hairpin Structure in a 13-mer Peptide that Binds a-Bungarotoxin with High…

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