SMTL ID : 5ceg.1

X-ray structure of toxin/anti-toxin complex from Mesorhizobium opportunistum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

hetero-4-4-mer

Ligands

14 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 4 residues within 4Å: Chain A: R.46, E.47, H.50, R.54 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.46, A:R.46, A:E.47, A:R.54 Water bridges: A:E.47, A:R.54 GOL.4: 5 residues within 4Å: Chain A: R.49 Chain B: R.110 Chain E: E.27, Y.28, E.37 7 PLIP interactions: 5 interactions with chain E, 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: E:E.27, E:Y.28, B:R.110 Water bridges: E:E.27, E:E.27, E:E.27, A:R.49 GOL.5: 9 residues within 4Å: Chain B: I.32, M.35, I.36, Y.47, F.83, D.108, R.110 Chain E: E.33, R.36 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain B Hydrogen bonds: E:R.36, B:D.108, B:R.110 GOL.8: 3 residues within 4Å: Chain C: D.61, K.64, A.65 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.61 GOL.10: 7 residues within 4Å: Chain A: R.49, D.52, I.53 Chain D: R.68, R.115, L.116, F.117 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.68, D:R.68 GOL.11: 10 residues within 4Å: Chain D: I.32, M.35, I.36, Y.47, F.83, D.108, R.110, R.111 Chain G: E.33, R.36 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain G Hydrogen bonds: D:D.108, D:D.108, D:R.110, D:R.111, D:R.111, G:E.33, G:R.36 GOL.12: 5 residues within 4Å: Chain D: D.28, V.106, V.107, D.108, D.112 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:D.28, D:D.28, D:R.105, D:D.108, D:D.108, D:D.112, A:R.55 Water bridges: D:R.111, D:R.111 GOL.17: 4 residues within 4Å: Chain E: R.46, E.47, H.50, R.54 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:R.46, E:R.46, E:E.47, E:R.54 Water bridges: E:E.47, E:R.54 GOL.20: 5 residues within 4Å: Chain A: E.27, Y.28, E.37 Chain E: R.49 Chain F: R.110 7 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 5 interactions with chain A Water bridges: E:R.49, A:E.27, A:E.27, A:E.27 Hydrogen bonds: F:R.110, A:E.27, A:Y.28 GOL.21: 9 residues within 4Å: Chain A: E.33, R.36 Chain F: I.32, M.35, I.36, Y.47, F.83, D.108, R.110 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:D.108, F:R.110, A:R.36 GOL.24: 3 residues within 4Å: Chain G: D.61, K.64, A.65 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:D.61 GOL.26: 7 residues within 4Å: Chain E: R.49, D.52, I.53 Chain H: R.68, R.115, L.116, F.117 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.68, H:R.68 GOL.27: 10 residues within 4Å: Chain C: E.33, R.36 Chain H: I.32, M.35, I.36, Y.47, F.83, D.108, R.110, R.111 7 PLIP interactions: 2 interactions with chain C, 5 interactions with chain H Hydrogen bonds: C:E.33, C:R.36, H:D.108, H:D.108, H:R.110, H:R.111, H:R.111 GOL.28: 5 residues within 4Å: Chain H: D.28, V.106, V.107, D.108, D.112 9 PLIP interactions: 8 interactions with chain H, 1 interactions with chain E Hydrogen bonds: H:D.28, H:D.28, H:R.105, H:D.108, H:D.108, H:D.112, E:R.55 Water bridges: H:R.111, H:R.111

16 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 1 residues within 4Å: Chain A: R.57 Ligand excluded by PLIP IOD.3: 1 residues within 4Å: Chain A: W.60 Ligand excluded by PLIP IOD.7: 2 residues within 4Å: Chain B: R.68 Chain C: L.56 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain B: R.115 Chain C: K.45, R.49 Ligand excluded by PLIP IOD.13: 1 residues within 4Å: Chain D: L.116 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain D: M.77, V.79, F.117 Ligand excluded by PLIP IOD.15: 4 residues within 4Å: Chain B: Q.61 Chain D: Q.61, P.62, R.63 Ligand excluded by PLIP IOD.16: 3 residues within 4Å: Chain B: R.115 Chain D: N.114, R.115 Ligand excluded by PLIP IOD.18: 1 residues within 4Å: Chain E: R.57 Ligand excluded by PLIP IOD.19: 1 residues within 4Å: Chain E: W.60 Ligand excluded by PLIP IOD.23: 2 residues within 4Å: Chain F: R.68 Chain G: L.56 Ligand excluded by PLIP IOD.25: 3 residues within 4Å: Chain F: R.115 Chain G: K.45, R.49 Ligand excluded by PLIP IOD.29: 1 residues within 4Å: Chain H: L.116 Ligand excluded by PLIP IOD.30: 3 residues within 4Å: Chain H: M.77, V.79, F.117 Ligand excluded by PLIP IOD.31: 4 residues within 4Å: Chain F: Q.61 Chain H: Q.61, P.62, R.63 Ligand excluded by PLIP IOD.32: 3 residues within 4Å: Chain F: R.115 Chain H: N.114, R.115 Ligand excluded by PLIP

2 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain B: G.109, R.110, L.113, L.116, F.117 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.113 NA.22: 5 residues within 4Å: Chain F: G.109, R.110, L.113, L.116, F.117 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:F.117

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Aakre, C.D. et al., Evolving New Protein-Protein Interaction Specificity through Promiscuous Intermediates. Cell (2015)

Release Date

2015-11-11

Peptides

Addiction module antidote protein, CopG/Arc/MetJ family: ACEG
Plasmid stabilization system: BDFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

B
B

D
D

F
B

H
D

Addiction module antidote protein, CopG/Arc/MetJ family

Plasmid stabilization system