SMTL ID : 7aer.1

Rebuilt and re-refined PDB entry 5yep: tri-AMPylated Shewanella oneidensis HEPN toxin in complex with MNT antitoxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-1-3-mer

Ligands

6 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)(Non-covalent)

AMP.1: 7 residues within 4Å: Chain B: R.70, G.95, N.98, I.99, Y.104, Q.105 Ligands: AMP.2 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.70, B:N.98, B:Q.105 Salt bridges: B:R.70 AMP.2: 11 residues within 4Å: Chain B: K.92, G.95, L.96, I.99, Q.105, E.106, L.107, N.108, I.111 Ligands: AMP.1, AMP.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.106, B:N.108 Salt bridges: B:R.70 AMP.3: 7 residues within 4Å: Chain B: K.92, N.108, D.110, I.111, H.114, H.119 Ligands: AMP.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.108, B:H.119 Salt bridges: B:K.92 AMP.4: 9 residues within 4Å: Chain A: T.49, R.76, F.103, K.106 Chain C: G.95, N.98, Y.104, Q.105 Ligands: AMP.5 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.98, C:Q.105, A:K.106, A:K.106 pi-Stacking: C:Y.104, C:Y.104 Salt bridges: A:K.106 pi-Cation interactions: A:R.76 AMP.5: 10 residues within 4Å: Chain C: K.92, G.95, L.96, Q.105, E.106, L.107, N.108, I.111 Ligands: AMP.4, AMP.6 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.96, C:E.106, C:N.108 AMP.6: 6 residues within 4Å: Chain C: N.108, D.110, I.111, H.114, H.119 Ligands: AMP.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.108, C:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Songailiene, I. et al., HEPN-MNT Toxin-Antitoxin System: The HEPN Ribonuclease Is Neutralized by OligoAMPylation. Mol.Cell (2020)

Release Date

2020-12-30

Peptides

Toxin-antitoxin system antidote Mnt family: A
Toxin-antitoxin system toxin HepN family: BCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Toxin-antitoxin system antidote Mnt family

Toxin-antitoxin system toxin HepN family

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