SMTL ID : 7n7u.1

Crystal Structure of SARS-CoV-2 NendoU in complex with LIZA-7

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.06 Å

Oligo State

homo-hexamer

Ligands

6 x 0MI: 1-[(2~{R},4~{S},5~{R})-5-[[(azanylidene-$l^{4}-azanylidene)amino]methyl]-4-oxidanyl-oxolan-2-yl]-5-methyl-pyrimidine-2,4-dione(Non-covalent)

0MI.1: 9 residues within 4Å: Chain A: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 Chain B: E.267, E.269 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:W.61, A:W.89, A:D.94 Hydrogen bonds: A:E.47, A:E.47, B:E.267, B:E.267, B:E.269 Water bridges: A:Y.91, A:Y.91, A:Y.91, A:Y.91, A:D.94 0MI.2: 9 residues within 4Å: Chain B: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 Chain C: E.267, E.269 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:W.61, B:W.89, B:D.94 Hydrogen bonds: B:E.47, B:E.47, C:E.267, C:E.269, C:E.269 Water bridges: B:Y.91, B:Y.91, B:Y.91, B:Y.91, B:D.94 0MI.3: 9 residues within 4Å: Chain A: E.267, E.269 Chain C: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 12 PLIP interactions: 10 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: C:W.61, C:W.89, C:D.94 Hydrogen bonds: C:E.47, C:E.47, A:E.267, A:E.269 Water bridges: C:Y.91, C:Y.91, C:Y.91, C:Y.91, C:D.94 0MI.4: 8 residues within 4Å: Chain D: F.46, E.47, W.61, W.89, Y.91, D.94 Chain F: E.267, E.269 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:W.89, D:D.94 Hydrogen bonds: D:E.47, D:E.47, D:Y.91, D:D.94, F:E.269, F:E.269 0MI.5: 8 residues within 4Å: Chain D: E.267, E.269 Chain E: F.46, E.47, W.61, W.89, Y.91, D.94 8 PLIP interactions: 2 interactions with chain D, 6 interactions with chain E Hydrogen bonds: D:E.267, D:E.269, E:E.47, E:E.47, E:Y.91, E:D.94 Hydrophobic interactions: E:W.89, E:D.94 0MI.6: 8 residues within 4Å: Chain E: E.267, E.269 Chain F: F.46, E.47, W.61, W.89, Y.91, D.94 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:W.89, F:D.94 Hydrogen bonds: F:E.47, F:E.47, F:Y.91, F:D.94, E:E.267, E:E.269

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoy, A.S. et al., Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res. (2023)

Release Date

2021-09-08

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Uridylate-specific endoribonuclease

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