SMTL ID : 7ae6.1

Crystal structure of di-AMPylated HEPN(R102A) toxin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

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

AMP.1: 6 residues within 4Å: Chain A: F.75, P.97, G.100, N.103, Y.109 Ligands: AMP.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:P.97, A:N.103 Water bridges: A:E.76 pi-Stacking: A:F.75, A:F.75 AMP.2: 10 residues within 4Å: Chain A: P.97, L.101, R.104, D.111, I.112, D.113, Q.116, V.117 Ligands: AMP.1, EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.104, A:D.111, A:D.113 Salt bridges: A:R.104 pi-Cation interactions: A:R.104 AMP.6: 7 residues within 4Å: Chain B: F.75, P.97, G.100, N.103, Y.109 Ligands: AMP.7, EDO.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:P.97, B:N.103 pi-Stacking: B:F.75, B:F.75 AMP.7: 11 residues within 4Å: Chain B: P.97, L.101, R.104, D.111, I.112, D.113, Q.116, V.117, A.120 Ligands: AMP.6, EDO.9 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.104, B:D.111, B:D.113, B:Q.116 Water bridges: B:R.104, B:Q.116

6 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 10 residues within 4Å: Chain A: Q.94, I.95, S.98, L.101, A.120, F.123, A.124, Q.127, Y.128 Ligands: EDO.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.94, A:Q.127 EDO.4: 7 residues within 4Å: Chain A: Q.94, P.97, S.98, F.123, Q.127 Ligands: AMP.2, EDO.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.127 Water bridges: A:P.97 EDO.5: 6 residues within 4Å: Chain A: F.26, E.27, I.29, F.118, I.121, S.122 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.29, A:I.29, A:S.122, A:S.122 EDO.8: 1 residues within 4Å: Chain B: D.21 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.21 EDO.9: 6 residues within 4Å: Chain B: S.98, L.101, F.123, A.124, Q.127 Ligands: AMP.7 No protein-ligand interaction detected (PLIP) EDO.10: 2 residues within 4Å: Chain B: E.76 Ligands: AMP.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.76

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

HEPN toxin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

HEPN toxin

Related Entries With Identical Sequence