SMTL ID : 7k1l.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-2',3'-Vanadate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-hexamer

Ligands

6 x UVC: URIDINE-2',3'-VANADATE(Non-covalent)

UVC.1: 14 residues within 4Å: Chain A: H.258, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 Ligands: ACT.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.366 Hydrogen bonds: A:G.271, A:K.313, A:S.317, A:S.317, A:S.317, A:T.364 Water bridges: A:Y.366, A:Y.366 UVC.6: 14 residues within 4Å: Chain B: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.366 Hydrogen bonds: B:Q.268, B:G.271, B:K.313, B:S.317, B:S.317, B:S.317, B:T.364, B:T.364 UVC.8: 14 residues within 4Å: Chain C: H.258, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 Ligands: ACT.9 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:Y.366 Hydrogen bonds: C:G.271, C:K.313, C:S.317, C:S.317, C:S.317, C:T.364 Water bridges: C:Y.366, C:Y.366 UVC.13: 14 residues within 4Å: Chain D: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.366 Hydrogen bonds: D:Q.268, D:G.271, D:K.313, D:S.317, D:S.317, D:S.317, D:T.364, D:T.364 UVC.15: 14 residues within 4Å: Chain E: H.258, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 Ligands: ACT.16 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:Y.366 Hydrogen bonds: E:G.271, E:K.313, E:S.317, E:S.317, E:S.317, E:T.364 Water bridges: E:Y.366, E:Y.366 UVC.20: 14 residues within 4Å: Chain F: H.258, Q.268, L.269, G.270, G.271, H.273, K.313, V.315, C.316, S.317, T.364, Y.366, P.367, K.368 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:Y.366 Hydrogen bonds: F:Q.268, F:G.271, F:K.313, F:S.317, F:S.317, F:S.317, F:T.364, F:T.364

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 1 residues within 4Å: Ligands: UVC.1 No protein-ligand interaction detected (PLIP) ACT.3: 3 residues within 4Å: Chain A: D.102, P.142, T.144 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.144 ACT.9: 1 residues within 4Å: Ligands: UVC.8 No protein-ligand interaction detected (PLIP) ACT.10: 3 residues within 4Å: Chain C: D.102, P.142, T.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:T.144 ACT.16: 1 residues within 4Å: Ligands: UVC.15 No protein-ligand interaction detected (PLIP) ACT.17: 3 residues within 4Å: Chain E: D.102, P.142, T.144 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:T.144

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 3 residues within 4Å: Chain A: T.72 Chain B: L.73, P.74 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Water bridges: A:T.72, A:T.72, B:T.72, B:T.72 EDO.11: 3 residues within 4Å: Chain C: T.72 Chain D: L.73, P.74 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Water bridges: D:T.72, D:T.72, C:T.72, C:T.72 EDO.18: 3 residues within 4Å: Chain E: T.72 Chain F: L.73, P.74 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Water bridges: F:T.72, F:T.72, E:T.72, E:T.72

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: F.67, E.68, K.70, D.115 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.68, A:D.115 Water bridges: A:K.70 SO4.7: 4 residues within 4Å: Chain B: F.67, E.68, K.70, D.115 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.68, B:E.68, B:D.115 Water bridges: B:E.65, B:K.70 SO4.12: 4 residues within 4Å: Chain C: F.67, E.68, K.70, D.115 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.68, C:D.115 Water bridges: C:K.70 SO4.14: 4 residues within 4Å: Chain D: F.67, E.68, K.70, D.115 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:E.68, D:E.68, D:D.115 Water bridges: D:E.65, D:K.70 SO4.19: 4 residues within 4Å: Chain E: F.67, E.68, K.70, D.115 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.68, E:D.115 Water bridges: E:K.70 SO4.21: 4 residues within 4Å: Chain F: F.67, E.68, K.70, D.115 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:E.68, F:E.68, F:D.115 Water bridges: F:E.65, F:K.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2. Commun Biol (2021)

Release Date

2020-09-23

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

Uridylate-specific endoribonuclease

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