SMTL ID : 5s6y.1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with Z56900771

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: 10 residues within 4Å: Chain A: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 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: 10 residues within 4Å: Chain B: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 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: 10 residues within 4Å: Chain C: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 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:H.252 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:H.252 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:H.252 Salt bridges: F:H.237, F:H.237, F:H.252, F:K.292, F:K.292, F:K.292

6 x WUJ: N-[(furan-2-yl)methyl]urea(Non-covalent)

WUJ.2: 8 residues within 4Å: Chain A: Q.155, P.156, S.157, V.158, Q.191, L.192, P.193, E.194 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Q.155 Hydrogen bonds: A:V.158, A:L.192, A:P.193 Water bridges: A:Q.191, A:T.195 WUJ.4: 8 residues within 4Å: Chain B: Q.155, P.156, S.157, V.158, Q.191, L.192, P.193, E.194 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Q.155 Hydrogen bonds: B:V.158, B:L.192, B:P.193 Water bridges: B:Q.191, B:T.195 WUJ.6: 8 residues within 4Å: Chain C: Q.155, P.156, S.157, V.158, Q.191, L.192, P.193, E.194 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Q.155 Hydrogen bonds: C:V.158, C:L.192, C:P.193 Water bridges: C:Q.191, C:T.195 WUJ.8: 4 residues within 4Å: Chain D: V.185, D.186, V.188, Q.190 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:D.186, D:V.188 Hydrogen bonds: D:D.186, D:D.186, D:D.186 WUJ.10: 4 residues within 4Å: Chain E: V.185, D.186, V.188, Q.190 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:D.186, E:V.188 Hydrogen bonds: E:D.186, E:D.186, E:D.186 WUJ.12: 4 residues within 4Å: Chain F: V.185, D.186, V.188, Q.190 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:D.186, F:V.188 Hydrogen bonds: F:D.186, F:D.186, F:D.186

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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