SMTL ID : 7k1o.1

Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

6 x VQV: 1-(3,5-di-O-phosphono-alpha-L-xylofuranosyl)pyrimidine-2,4(1H,3H)-dione(Non-covalent)

VQV.1: 10 residues within 4Å: Chain A: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.268, A:G.271, A:T.364 Salt bridges: A:H.258, A:H.273, A:K.313 pi-Stacking: A:W.356, A:W.356 VQV.3: 10 residues within 4Å: Chain B: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.271 Salt bridges: B:H.258, B:H.273, B:K.313 pi-Stacking: B:W.356 VQV.5: 11 residues within 4Å: Chain C: H.258, Q.268, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.6 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:Q.268, C:L.269, C:G.271, C:E.363, C:T.364 Salt bridges: C:H.258, C:H.273, C:K.313 pi-Stacking: C:W.356, C:W.356 VQV.7: 10 residues within 4Å: Chain D: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.8 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.268, D:G.271, D:E.363, D:Y.366 Salt bridges: D:H.258, D:H.273, D:K.313 pi-Stacking: D:W.356, D:W.356 VQV.9: 10 residues within 4Å: Chain E: H.258, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.10 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.271, E:T.364 Salt bridges: E:H.258, E:H.273, E:K.313 pi-Stacking: E:W.356 VQV.11: 11 residues within 4Å: Chain F: H.258, Q.268, G.270, G.271, H.273, K.313, W.356, E.363, T.364, Y.366 Ligands: EDO.12 11 PLIP interactions: 11 interactions with chain F Hydrogen bonds: F:Q.268, F:L.269, F:G.271, F:E.363, F:E.363, F:Y.366 Salt bridges: F:H.258, F:H.273, F:K.313 pi-Stacking: F:W.356, F:W.356

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

EDO.2: 7 residues within 4Å: Chain A: H.273, K.313, V.315, C.316, S.317, Y.366 Ligands: VQV.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.317, A:S.317 EDO.4: 7 residues within 4Å: Chain B: H.273, K.313, V.315, C.316, S.317, Y.366 Ligands: VQV.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.317, B:S.317 EDO.6: 6 residues within 4Å: Chain C: H.273, V.315, C.316, S.317, Y.366 Ligands: VQV.5 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:H.273, C:S.317 EDO.8: 7 residues within 4Å: Chain D: H.273, K.313, V.315, C.316, S.317, Y.366 Ligands: VQV.7 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.317, D:S.317 EDO.10: 7 residues within 4Å: Chain E: H.273, K.313, V.315, C.316, S.317, Y.366 Ligands: VQV.9 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.317, E:S.317 EDO.12: 6 residues within 4Å: Chain F: H.273, V.315, C.316, S.317, Y.366 Ligands: VQV.11 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.317, F:S.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, Y. et al., Crystal Structure of NSP15 Endoribonuclease from SARS CoV-2 in the Complex with Uridine-3',5'-Diphosphate. To Be Published

Release Date

2020-09-23

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Uridylate-specific endoribonuclease

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