SMTL ID : 9ea9.1

Crystal structure of BoNT/A-NTNH-HA70 -VHH_F12-VHH_H7-Fab_NTNH complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.93 Å

Oligo State

hetero-1-1-1-1-5-1-1-1-1-1-mer

Ligands

10 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: K.779, N.940, K.1077, E.1078 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.940, A:E.1078 Salt bridges: A:K.772, A:K.779 SO4.2: 5 residues within 4Å: Chain A: S.622, T.623 Chain B: T.576, Q.577, E.578 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.623, B:E.578 SO4.3: 3 residues within 4Å: Chain A: Y.1165 Chain B: N.1100, N.1102 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.1100, B:N.1102 SO4.4: 1 residues within 4Å: Chain A: N.1080 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.1080 Salt bridges: A:K.779 SO4.7: 2 residues within 4Å: Chain B: N.335, N.337 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.335, B:N.337 SO4.8: 6 residues within 4Å: Chain B: D.60, E.400, G.420, G.422, K.486, T.488 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.420, B:G.422 Salt bridges: B:K.486 SO4.9: 2 residues within 4Å: Chain B: S.50, L.51 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.50, B:L.51 SO4.10: 3 residues within 4Å: Chain B: I.113, R.151, Y.474 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.474 Salt bridges: B:R.151 SO4.13: 4 residues within 4Å: Chain G: N.18, S.20, T.22 Chain H: K.476 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:N.18 Salt bridges: H:K.476 SO4.14: 4 residues within 4Å: Chain H: N.615, Y.616, N.617, R.619 4 PLIP interactions: 4 interactions with chain H Hydrogen bonds: H:N.615, H:Y.616, H:N.617 Salt bridges: H:R.619

1 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: H.223, Q.224, H.227, E.262 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.223, A:H.227, A:E.262, A:E.262

10 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 2 residues within 4Å: Chain A: H.1253, Q.1254 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain A: N.1245 Chain B: G.847 No protein-ligand interaction detected (PLIP) MG.12: 2 residues within 4Å: Chain F: S.463, R.528 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain E: N.94 Chain H: R.227 No protein-ligand interaction detected (PLIP) MG.16: 1 residues within 4Å: Chain H: F.362 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain H: T.527, R.619 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Chain H: S.390, D.391 No protein-ligand interaction detected (PLIP) MG.19: 1 residues within 4Å: Chain H: R.499 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain H: S.463, R.528 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:S.463 MG.21: 3 residues within 4Å: Chain G: R.33, D.36 Chain J: K.308 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lam, K.H. et al., A nut-and-bolt assembly of the bimodular large progenitor botulinum neurotoxin complex. Sci Adv (2025)

Release Date

2025-09-17

Peptides

Botulinum neurotoxin type A: A
Non-toxic nonhemagglutinin type A: B
Nanobody ciA-F12: C
Nanobody ciA-H7: D
HA-70: EFGIJ
HA70/A1: H
anti-NTNH Fab: K
anti-NTNH Fab: L
anti-NTNH Fab: M
anti-NTNH Fab: N

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
I

F
J

G
D

I
G

J
H

H
E

K
K

L
M

M
N

N
L

Botulinum neurotoxin type A

Non-toxic nonhemagglutinin type A

Nanobody ciA-F12

Nanobody ciA-H7

HA-70

HA70/A1

anti-NTNH Fab

anti-NTNH Fab

anti-NTNH Fab

anti-NTNH Fab

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