SMTL ID : 7n83.1

Crystal Structure of SARS-CoV-2 NendoU in complex with Z2443429438

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 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.6: 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.11: 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.16: 9 residues within 4Å: Chain D: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 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.20: 9 residues within 4Å: Chain E: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 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.24: 9 residues within 4Å: Chain F: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 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

21 x WNM: (3S)-1-(phenylsulfonyl)pyrrolidin-3-amine(Non-covalent)

WNM.2: 8 residues within 4Å: Chain A: I.272, N.280, L.348, Q.349 Chain C: V.13, N.14, V.38, D.39 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.348 Hydrogen bonds: A:N.280, A:L.348 WNM.3: 7 residues within 4Å: Chain A: G.172, E.173, A.174, V.175, K.176 Chain B: S.244, H.245 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Water bridges: B:H.245, B:S.246, A:K.176 WNM.4: 7 residues within 4Å: Chain A: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:N.85 Hydrogen bonds: A:K.63, A:N.85, A:G.103 pi-Stacking: A:F.18 WNM.5: 9 residues within 4Å: Chain A: N.77, L.78, K.183, V.185, Q.190, Q.191, L.192, P.193, Y.327 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.78, A:L.192 Hydrogen bonds: A:Q.190 WNM.7: 8 residues within 4Å: Chain A: V.13, N.14, V.38, D.39 Chain B: I.272, N.280, L.348, Q.349 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.348 Hydrogen bonds: B:N.280, B:L.348 WNM.8: 7 residues within 4Å: Chain B: G.172, E.173, A.174, V.175, K.176 Chain C: S.244, H.245 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Water bridges: C:H.245, C:S.246, B:K.176 WNM.9: 7 residues within 4Å: Chain B: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:N.85 Hydrogen bonds: B:K.63, B:N.85, B:G.103 pi-Stacking: B:F.18 WNM.10: 9 residues within 4Å: Chain B: N.77, L.78, K.183, V.185, Q.190, Q.191, L.192, P.193, Y.327 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.78, B:L.192 Hydrogen bonds: B:Q.190 WNM.12: 8 residues within 4Å: Chain B: V.13, N.14, V.38, D.39 Chain C: I.272, N.280, L.348, Q.349 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.348 Hydrogen bonds: C:N.280, C:L.348 WNM.13: 7 residues within 4Å: Chain A: S.244, H.245 Chain C: G.172, E.173, A.174, V.175, K.176 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C Water bridges: A:H.245, A:S.246, C:K.176 WNM.14: 7 residues within 4Å: Chain C: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:N.85 Hydrogen bonds: C:K.63, C:N.85, C:G.103 pi-Stacking: C:F.18 WNM.15: 9 residues within 4Å: Chain C: N.77, L.78, K.183, V.185, Q.190, Q.191, L.192, P.193, Y.327 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.78, C:L.192 Hydrogen bonds: C:Q.190 WNM.17: 8 residues within 4Å: Chain D: I.272, N.280, L.348, Q.349 Chain E: V.13, N.14, V.38, D.39 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:L.348 Hydrogen bonds: D:N.280, D:L.348 WNM.18: 7 residues within 4Å: Chain D: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:N.85 Hydrogen bonds: D:K.63, D:N.85, D:G.103 pi-Stacking: D:F.18 WNM.19: 7 residues within 4Å: Chain D: G.172, E.173, A.174, V.175, K.176 Chain F: S.244, H.245 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain D Water bridges: F:H.245, F:S.246, D:K.176, D:K.176 Hydrogen bonds: D:A.174 WNM.21: 8 residues within 4Å: Chain E: I.272, N.280, L.348, Q.349 Chain F: V.13, N.14, V.38, D.39 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.348 Hydrogen bonds: E:N.280, E:L.348 WNM.22: 7 residues within 4Å: Chain E: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:N.85 Hydrogen bonds: E:K.63, E:N.85, E:G.103 pi-Stacking: E:F.18 WNM.23: 7 residues within 4Å: Chain D: S.244, H.245 Chain E: G.172, E.173, A.174, V.175, K.176 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:A.174 Water bridges: E:K.176, E:K.176, D:H.245, D:S.246 WNM.25: 8 residues within 4Å: Chain D: V.13, N.14, V.38, D.39 Chain F: I.272, N.280, L.348, Q.349 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.348 Hydrogen bonds: F:N.280, F:L.348 WNM.26: 7 residues within 4Å: Chain F: F.18, D.19, G.20, K.63, N.85, G.103, V.104 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:N.85 Hydrogen bonds: F:K.63, F:N.85, F:G.103 pi-Stacking: F:F.18 WNM.27: 7 residues within 4Å: Chain E: S.244, H.245 Chain F: G.172, E.173, A.174, V.175, K.176 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain F Water bridges: E:H.245, E:S.246, F:K.176, F:K.176 Hydrogen bonds: F:A.174

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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