8DA1: Krait alpha-neurotoxin

Crystal structure of Krait alpha-neurotoxin in complex with Centi-LNX-D09 antibody. Determined by X-ray diffraction at 2.67 Å resolution. Released 14 Jun 2023.

Method: X-ray diffraction
Resolution: 2.67 Å
Organisms: Homo sapiens, Bungarus multicinctus
Chains: 3
Atoms: 3,882
Mol. weight: 56.48 kDa
Released: 14 Jun 2023

Explore 8DA1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8DA1 contains 21 α-helices and 51 β-strands across 3 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 A: 8 helices, 21 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	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	85-90	6	2
α-helix	96	1
β-strand	97-98	2	2
β-strand	102-106	5	2
β-strand	111	1	3
α-helix	112-113	2
β-strand	114-118	5	4
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	4
β-strand	140	1	3
β-strand	144-150	7	5
β-strand	153-154	2	5
β-strand	159-163	5	4
α-helix	164-167	4
β-strand	173-182	10	4
α-helix	183-187	5
β-strand	191-198	8	5
β-strand	205-210	6	5

Chain B: 10 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	6
β-strand	11-12	2	7
β-strand	18-25	8	6
α-helix	29-31	3
β-strand	34-40	7	2
β-strand	44-51	8	2
β-strand	57-59	3	2
α-helix	61-63	3
β-strand	67-72	6	6
β-strand	77-82	6	6
α-helix	84-86	3
β-strand	88-99	12	2
β-strand	100	1	8
β-strand	100D-103	10	2
β-strand	107-109	3	2
β-strand	110-111	2	7
α-helix	114-116	3
β-strand	117	1	9
α-helix	118-119	2
β-strand	120-124	5	10
α-helix	128-130	3
β-strand	131-132	2	10
β-strand	135-145	11	10
β-strand	146	1	9
β-strand	151-154	4	11
α-helix	155-157	3
β-strand	159	1	11
β-strand	163-165	3	10
α-helix	166-168	3
β-strand	169-170	2	10
β-strand	176-185	10	10
α-helix	186-190	5
β-strand	195-200	6	11
α-helix	201-203	3
β-strand	205-210	6	11

Chain I: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	12
β-strand	12-15	4	12
α-helix	16-17	2
β-strand	22-28	7	8
α-helix	33-36	4
β-strand	39-45	7	8
α-helix	48-51	4
β-strand	56-60	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Centi-LNX-D09 Fab light chain	A	protein	214	Homo sapiens
Centi-LNX-D09 Fab heavy chain	B	protein	237	Homo sapiens
Alpha-bungarotoxin	I	protein	74	Bungarus multicinctus	P60615 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8DA1_1 Centi-LNX-D09 Fab light chain (chains A)
EIVLTQSPSSLSASVGDRVTITCQASQDISNYLNWYQQKPGKAPKLLIYAASSLESGVPS
RFSGSGSGTDFTLTISSQQPEDFATYYCQQANSFPYTFGQGTKVEIKRTVAAPSVFIFPP
SDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLT
LSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B), FASTA

>8DA1_2 Centi-LNX-D09 Fab heavy chain (chains B)
EVQLVESGGGFVQPGGSLRLSCAASGFTFSNFDMHWVRQSPGKGLEWVSGLDHSGGAHYA
GSVKGRFTISREDAKNSLDLQMNNLRVDDTAVYFCVRGTLYHYTSGSYYSDAFDIWGQGT
LVTVSSASVKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCDKTHTGLE

Sequence of entity 3 (I), FASTA

>8DA1_3 Alpha-bungarotoxin (chains I)
IVCHTTATSPISAVTCPPGENLCYRKMWCDAFCSSRGKVVELGCAATCPSKKPYEEVTCC
STDKCNPHPKQRPG

Primary citation

Venom protection by antibody from a snakebite hyperimmune subject. Glanville, J., Andrade, J., Bellin, M. et al. To be published.

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

9FYS 1.32 Å, D11 mAbs bound to alpha-Bungarotoxin
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…
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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