SMTL ID : 5sae.1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z3219959731

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.12 Å

Oligo State

homo-hexamer

Ligands

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 9 residues within 4Å: Chain A: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.345 Hydrogen bonds: A:Q.247, A:G.250, A:Y.345 Water bridges: A:V.294 Salt bridges: A:H.237, A:H.237, A:H.252, A:K.292, A:K.292 CIT.3: 9 residues within 4Å: Chain B: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.345 Hydrogen bonds: B:Q.247, B:G.250, B:Y.345 Water bridges: B:V.294 Salt bridges: B:H.237, B:H.237, B:H.252, B:K.292, B:K.292 CIT.5: 9 residues within 4Å: Chain C: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.345 Hydrogen bonds: C:Q.247, C:G.250, C:Y.345 Water bridges: C:V.294 Salt bridges: C:H.237, C:H.237, C:H.252, C:K.292, C:K.292 CIT.7: 10 residues within 4Å: Chain D: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.345 Hydrogen bonds: D:Q.247, D:G.250, D:T.343, D:T.343 Water bridges: D:Y.345 Salt bridges: D:H.237, D:H.237, D:H.252, D:K.292, D:K.292, D:K.292 CIT.9: 10 residues within 4Å: Chain E: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:Y.345 Hydrogen bonds: E:Q.247, E:G.250, E:T.343, E:T.343 Water bridges: E:Y.345 Salt bridges: E:H.237, E:H.237, E:H.252, E:K.292, E:K.292, E:K.292 CIT.11: 10 residues within 4Å: Chain F: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 12 PLIP interactions: 12 interactions with chain F Hydrophobic interactions: F:Y.345 Hydrogen bonds: F:Q.247, F:G.250, F:T.343, F:T.343 Water bridges: F:Y.345 Salt bridges: F:H.237, F:H.237, F:H.252, F:K.292, F:K.292, F:K.292

6 x W3G: pyridazin-3(2H)-one(Non-covalent)

W3G.2: 5 residues within 4Å: Chain A: F.46, E.47, W.61, W.89, D.94 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.46 Hydrogen bonds: A:E.47, A:E.47 Water bridges: A:K.49 pi-Stacking: A:W.61 W3G.4: 5 residues within 4Å: Chain B: F.46, E.47, W.61, W.89, D.94 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.46 Hydrogen bonds: B:E.47, B:E.47 Water bridges: B:K.49 pi-Stacking: B:W.61 W3G.6: 5 residues within 4Å: Chain C: F.46, E.47, W.61, W.89, D.94 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.46 Hydrogen bonds: C:E.47, C:E.47 Water bridges: C:K.49 pi-Stacking: C:W.61 W3G.8: 5 residues within 4Å: Chain D: F.46, E.47, W.61, W.89, D.94 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.46 Hydrogen bonds: D:E.47, D:E.47 Water bridges: D:K.49, D:K.49 pi-Stacking: D:W.61 W3G.10: 5 residues within 4Å: Chain E: F.46, E.47, W.61, W.89, D.94 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.46 Hydrogen bonds: E:E.47, E:E.47 Water bridges: E:K.49, E:K.49 pi-Stacking: E:W.61 W3G.12: 5 residues within 4Å: Chain F: F.46, E.47, W.61, W.89, D.94 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.46 Hydrogen bonds: F:E.47, F:E.47 Water bridges: F:K.49, F:K.49 pi-Stacking: F:W.61

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

2021-06-09

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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