SMTL ID : 6x1b.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with the Product Nucleotide GpU.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-hexamer

Ligands

6 x G- U: DNA (5'-R(*GP*U)-3')(Non-covalent)

G-U.1: 12 residues within 4Å: Chain A: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368 Ligands: PO4.3 Protein-ligand interaction information (PLIP) not available G-U.2: 13 residues within 4Å: Chain B: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368, L.369 Ligands: PO4.7 Protein-ligand interaction information (PLIP) not available G-U.8: 12 residues within 4Å: Chain C: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368 Ligands: PO4.10 Protein-ligand interaction information (PLIP) not available G-U.9: 13 residues within 4Å: Chain D: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368, L.369 Ligands: PO4.14 Protein-ligand interaction information (PLIP) not available G-U.15: 12 residues within 4Å: Chain E: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368 Ligands: PO4.17 Protein-ligand interaction information (PLIP) not available G-U.16: 13 residues within 4Å: Chain F: Q.268, H.273, K.313, V.315, C.316, S.317, W.356, T.364, Y.366, P.367, K.368, L.369 Ligands: PO4.21 Protein-ligand interaction information (PLIP) not available

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 8 residues within 4Å: Chain A: H.258, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.1, G-U.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.271 Water bridges: A:L.269 Salt bridges: A:H.258, A:H.273, A:K.313 PO4.7: 9 residues within 4Å: Chain B: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.2, G-U.2 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.271, B:T.364 Water bridges: B:L.269 Salt bridges: B:H.258, B:H.273, B:K.313 PO4.10: 8 residues within 4Å: Chain C: H.258, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.8, G-U.8 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.271 Water bridges: C:L.269 Salt bridges: C:H.258, C:H.273, C:K.313 PO4.14: 9 residues within 4Å: Chain D: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.9, G-U.9 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.271, D:T.364 Water bridges: D:L.269 Salt bridges: D:H.258, D:H.273, D:K.313 PO4.17: 8 residues within 4Å: Chain E: H.258, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.15, G-U.15 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:G.271 Water bridges: E:L.269 Salt bridges: E:H.258, E:H.273, E:K.313 PO4.21: 9 residues within 4Å: Chain F: H.258, G.270, G.271, H.273, K.313, T.364, Y.366 Ligands: G-U.16, G-U.16 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.271, F:T.364 Water bridges: F:L.269 Salt bridges: F:H.258, F:H.273, F:K.313

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

EDO.4: 4 residues within 4Å: Chain B: V.172, K.173, G.174, L.175 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.172, B:G.174 EDO.5: 3 residues within 4Å: Chain B: T.136, E.137, T.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.136 Water bridges: B:T.138 EDO.6: 5 residues within 4Å: Chain B: S.267, Q.268, S.312, K.313, C.314 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.268 Water bridges: B:S.312, B:C.314 EDO.11: 4 residues within 4Å: Chain D: V.172, K.173, G.174, L.175 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:V.172, D:G.174 EDO.12: 3 residues within 4Å: Chain D: T.136, E.137, T.138 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:T.136 Water bridges: D:T.138 EDO.13: 5 residues within 4Å: Chain D: S.267, Q.268, S.312, K.313, C.314 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.268 Water bridges: D:S.312, D:C.314 EDO.18: 4 residues within 4Å: Chain F: V.172, K.173, G.174, L.175 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:V.172, F:G.174 EDO.19: 3 residues within 4Å: Chain F: T.136, E.137, T.138 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:T.136 Water bridges: F:T.138 EDO.20: 5 residues within 4Å: Chain F: S.267, Q.268, S.312, K.313, C.314 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.268 Water bridges: F:S.312, F:C.314

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

2020-05-27

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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