SMTL ID : 9lew.1

The crystal structure of DinJ-YafQ complex from Vibrio cholerae

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-8-8-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain B: P.60, R.69 Chain H: K.74 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain H Salt bridges: B:R.69, H:K.74 SO4.10: 3 residues within 4Å: Chain J: P.60, R.69 Chain P: K.74 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain J Salt bridges: P:K.74, J:R.69

16 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 2 residues within 4Å: Chain C: H.74, K.75 Ligand excluded by PLIP ACT.3: 4 residues within 4Å: Chain C: K.17, T.31 Chain F: H.72, P.75 Ligand excluded by PLIP ACT.4: 8 residues within 4Å: Chain A: I.43, N.44 Chain C: P.55 Chain D: D.70, H.72, V.78, Q.96, F.100 Ligand excluded by PLIP ACT.5: 2 residues within 4Å: Chain D: P.60, R.69 Ligand excluded by PLIP ACT.6: 4 residues within 4Å: Chain D: K.74 Chain F: D.58, P.60, R.69 Ligand excluded by PLIP ACT.7: 3 residues within 4Å: Chain E: T.10, R.11 Chain G: S.32 Ligand excluded by PLIP ACT.8: 7 residues within 4Å: Chain E: I.43 Chain G: P.55 Chain H: D.70, H.72, V.78, Q.96, F.100 Ligand excluded by PLIP ACT.9: 2 residues within 4Å: Chain H: P.60, R.69 Ligand excluded by PLIP ACT.11: 2 residues within 4Å: Chain K: H.74, K.75 Ligand excluded by PLIP ACT.12: 4 residues within 4Å: Chain K: K.17, T.31 Chain N: H.72, P.75 Ligand excluded by PLIP ACT.13: 8 residues within 4Å: Chain I: I.43, N.44 Chain K: P.55 Chain L: D.70, H.72, V.78, Q.96, F.100 Ligand excluded by PLIP ACT.14: 2 residues within 4Å: Chain L: P.60, R.69 Ligand excluded by PLIP ACT.15: 4 residues within 4Å: Chain L: K.74 Chain N: D.58, P.60, R.69 Ligand excluded by PLIP ACT.16: 3 residues within 4Å: Chain M: T.10, R.11 Chain O: S.32 Ligand excluded by PLIP ACT.17: 7 residues within 4Å: Chain M: I.43 Chain O: P.55 Chain P: D.70, H.72, V.78, Q.96, F.100 Ligand excluded by PLIP ACT.18: 2 residues within 4Å: Chain P: P.60, R.69 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mun, S.A. et al., Novel oligomerization state of DinJ-YafQ complex from Vibrio cholerae-Structural and biochemical insights. Int.J.Biol.Macromol. (2025)

Release Date

2025-07-30

Peptides

DNA-damage-inducible protein J: ACEGIKMO
Type II toxin-antitoxin system YafQ family toxin: BDFHJLNP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
A

K
C

M
E

O
G

B
B

D
D

F
F

H
H

J
B

L
D

N
F

P
H

DNA-damage-inducible protein J

Type II toxin-antitoxin system YafQ family toxin