SMTL ID : 5s6x.1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z2889976755

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-hexamer

Ligands

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

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

6 x WUG: 1-(2,4-dimethyl-1H-imidazol-5-yl)methanamine(Non-covalent)

WUG.2: 7 residues within 4Å: Chain A: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.46, A:W.61, A:Y.91 Hydrogen bonds: A:D.94, A:D.94 WUG.4: 7 residues within 4Å: Chain B: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.46, B:W.61, B:Y.91 Hydrogen bonds: B:D.94, B:D.94 WUG.6: 7 residues within 4Å: Chain C: L.45, F.46, E.47, W.61, W.89, Y.91, D.94 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.46, C:W.61, C:Y.91 Hydrogen bonds: C:D.94, C:D.94 WUG.8: 6 residues within 4Å: Chain D: L.45, F.46, E.47, W.61, W.89, Y.91 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:W.61, D:Y.91 Hydrogen bonds: D:E.47 Water bridges: D:E.47, D:E.47, D:K.49 WUG.10: 6 residues within 4Å: Chain E: L.45, F.46, E.47, W.61, W.89, Y.91 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.61, E:Y.91 Hydrogen bonds: E:E.47 Water bridges: E:E.47, E:E.47, E:K.49 WUG.12: 6 residues within 4Å: Chain F: L.45, F.46, E.47, W.61, W.89, Y.91 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:W.61, F:Y.91 Hydrogen bonds: F:E.47 Water bridges: F:E.47, F:E.47, F:K.49

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

2020-11-25

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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