SMTL ID : 8ver.1

Structure of YicC endoribonuclease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-hexamer

Ligands

12 x SO4: SULFATE ION

SO4.1: 6 residues within 4Å: Chain A: L.34, E.35, T.36, R.52, R.56 Chain B: R.27 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.36, A:T.36, A:T.36, A:R.52, B:R.27 Salt bridges: A:R.56 SO4.2: 3 residues within 4Å: Chain A: R.27, V.29, E.65 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.27, A:K.63 SO4.3: 5 residues within 4Å: Chain A: N.252, N.256, K.275 Chain C: F.246, Q.249 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain A Hydrogen bonds: C:Q.249, C:Q.249, A:N.252, A:N.256 Salt bridges: A:K.275 SO4.4: 4 residues within 4Å: Chain A: Q.249, N.252, R.282 Chain C: R.32 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:N.252, C:R.32 Salt bridges: A:R.282 SO4.5: 3 residues within 4Å: Chain A: R.5, R.58, I.144 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.5, A:R.58 SO4.6: 3 residues within 4Å: Chain A: R.32 Chain B: Q.249, R.282 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.282, A:R.32 SO4.7: 1 residues within 4Å: Chain C: R.282 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.282 SO4.8: 2 residues within 4Å: Chain C: R.5, R.58 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.5, C:R.58 SO4.9: 5 residues within 4Å: Chain D: E.35, T.36, R.52, R.56 Chain E: N.30 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.36, D:T.36 Salt bridges: D:R.52, D:R.56 SO4.10: 3 residues within 4Å: Chain D: Q.249, N.252, R.282 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.252 Salt bridges: D:R.282 SO4.11: 7 residues within 4Å: Chain D: N.252, N.256, K.275, E.279 Chain F: R.32, F.246, Q.249 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain F Hydrogen bonds: D:N.252, D:N.256, D:E.279, F:R.32, F:Q.249 Salt bridges: D:K.275 SO4.12: 2 residues within 4Å: Chain F: Q.249, R.282 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:R.282

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, R. et al., Structural insights into RNA cleavage by a novel family of bacterial RNases. Nucleic Acids Res. (2024)

Release Date

2024-09-04

Peptides

Endoribonuclease YicC: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Endoribonuclease YicC