SMTL ID : 7bxo.1

Crystal structure of the toxin-antitoxin with AMP-PNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.77 Å

Oligo State

hetero-2-6-mer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 15 residues within 4Å: Chain A: F.26, G.27, S.28, H.35, S.38, D.39, D.41, Q.85 Chain H: D.3, I.4, N.7, K.8, R.59 Ligands: MG.2, MG.3 8 PLIP interactions: 4 interactions with chain H, 4 interactions with chain A Hydrogen bonds: H:N.7, H:K.8, H:K.8, H:R.59, A:S.28, A:S.28, A:H.35, A:D.39 ANP.4: 20 residues within 4Å: Chain D: D.3, I.4, N.7, K.8, R.59 Chain E: F.26, G.27, S.28, H.35, S.38, D.39, D.41, V.81, Q.85, Q.89 Chain H: D.103, A.104, Q.105 Ligands: MG.5, MG.6 11 PLIP interactions: 4 interactions with chain D, 6 interactions with chain E, 1 interactions with chain H Hydrogen bonds: D:N.7, D:K.8, D:R.59, D:R.59, E:S.28, E:S.28, E:S.28, E:D.39, E:Q.89, E:Q.89, H:D.103

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.28, D.39, D.41 Ligands: ANP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.39, A:D.41 MG.3: 4 residues within 4Å: Chain A: D.39, D.41, D.71 Ligands: ANP.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.39, A:D.41, A:D.71 MG.5: 3 residues within 4Å: Chain E: D.39, D.41 Ligands: ANP.4 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.39, E:D.41 MG.6: 4 residues within 4Å: Chain E: D.39, D.41, D.71 Ligands: ANP.4 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.39, E:D.41

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yao, J. et al., Novel polyadenylylation-dependent neutralization mechanism of the HEPN/MNT toxin/antitoxin system. Nucleic Acids Res. (2020)

Release Date

2020-09-30

Peptides

Toxin-antitoxin system antidote Mnt family: AE
Toxin-antitoxin system toxin HepN family: BCDFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

B
B

C
C

D
D

F
F

G
G

H
H

Toxin-antitoxin system antidote Mnt family

Toxin-antitoxin system toxin HepN family

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