SMTL ID : 7k0r.1

Nucleotide bound SARS-CoV-2 Nsp15

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

6 x U5P: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U5P.1: 8 residues within 4Å: Chain A: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.265, A:S.309, A:S.309, A:S.309, A:Y.358 U5P.3: 8 residues within 4Å: Chain B: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.4 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.265, B:S.309, B:S.309, B:S.309, B:Y.358 U5P.5: 8 residues within 4Å: Chain C: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.6 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:H.265, C:S.309, C:S.309, C:S.309, C:Y.358 U5P.7: 8 residues within 4Å: Chain D: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.8 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:H.265, D:S.309, D:S.309, D:S.309, D:Y.358 U5P.9: 8 residues within 4Å: Chain E: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:H.265, E:S.309, E:S.309, E:S.309, E:Y.358 U5P.11: 8 residues within 4Å: Chain F: Q.260, H.265, K.305, V.307, C.308, S.309, Y.358 Ligands: PO4.12 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.265, F:S.309, F:S.309, F:S.309, F:Y.358

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

PO4.2: 7 residues within 4Å: Chain A: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.263 Salt bridges: A:H.250, A:H.265, A:K.305 PO4.4: 7 residues within 4Å: Chain B: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.263 Salt bridges: B:H.250, B:H.265, B:K.305 PO4.6: 7 residues within 4Å: Chain C: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.5 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:G.263 Salt bridges: C:H.250, C:H.265, C:K.305 PO4.8: 7 residues within 4Å: Chain D: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.7 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.263, D:T.356, D:T.356 Salt bridges: D:H.250, D:H.265, D:K.305 PO4.10: 7 residues within 4Å: Chain E: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.9 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.263, E:T.356, E:T.356 Salt bridges: E:H.250, E:H.265, E:K.305 PO4.12: 7 residues within 4Å: Chain F: H.250, G.262, G.263, H.265, K.305, T.356 Ligands: U5P.11 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.263, F:T.356, F:T.356 Salt bridges: F:H.250, F:H.265, F:K.305

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pillon, M.C. et al., Cryo-EM structures of the SARS-CoV-2 endoribonuclease Nsp15 reveal insight into nuclease specificity and dynamics. Nat Commun (2021)

Release Date

2020-12-09

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