SMTL ID : 7n33.1

SARS-CoV-2 Nsp15 endoribonuclease pre-cleavage state

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x UFT- A: RNA (5'-R(*A)-D(*(UFT))-R(P*A)-3')(Non-covalent)

UFT-A.1: 11 residues within 4Å: Chain A: H.250, Q.260, L.261, G.262, G.263, H.265, K.305, V.307, C.308, S.309, Y.358 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:Y.358 Hydrogen bonds: A:Q.260, A:S.309, A:S.309, A:S.309 Halogen bonds: A:K.305 UFT-A.2: 11 residues within 4Å: Chain B: H.250, Q.260, L.261, G.262, G.263, H.265, K.305, V.307, C.308, S.309, Y.358 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.358 Hydrogen bonds: B:Q.260, B:S.309, B:S.309, B:S.309 Halogen bonds: B:K.305 UFT-A.3: 11 residues within 4Å: Chain C: H.250, Q.260, L.261, G.262, G.263, H.265, K.305, V.307, C.308, S.309, Y.358 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Y.358 Hydrogen bonds: C:Q.260, C:S.309, C:S.309, C:S.309 Halogen bonds: C:K.305 UFT-A.4: 9 residues within 4Å: Chain D: H.250, G.263, H.265, K.305, V.307, C.308, S.309, T.356, Y.358 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Y.358 Hydrogen bonds: D:S.309, D:S.309, D:S.309 Halogen bonds: D:K.305 UFT-A.5: 9 residues within 4Å: Chain E: H.250, G.263, H.265, K.305, V.307, C.308, S.309, T.356, Y.358 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:Y.358 Hydrogen bonds: E:S.309, E:S.309, E:S.309 Halogen bonds: E:K.305 UFT-A.6: 9 residues within 4Å: Chain F: H.250, G.263, H.265, K.305, V.307, C.308, S.309, T.356, Y.358 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:Y.358 Hydrogen bonds: F:S.309, F:S.309, F:S.309 Halogen bonds: F:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frazier, M.N. et al., Characterization of SARS2 Nsp15 nuclease activity reveals it's mad about U. Nucleic Acids Res. (2021)

Release Date

2021-06-09

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Uridylate-specific endoribonuclease