SMTL ID : 5saf.1

PanDDA analysis group deposition -- Crystal Structure of SARS-CoV-2 NendoU in complex with EN300-321461

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-hexamer

Ligands

6 x CIT: CITRIC ACID(Non-functional Binders)

CIT.1: 11 residues within 4Å: Chain A: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 Ligands: WOY.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.345 Hydrogen bonds: A:Q.247, A:G.250, A:Y.345 Water bridges: A:V.294 Salt bridges: A:H.237, A:H.237, A:H.252, A:K.292, A:K.292 CIT.3: 11 residues within 4Å: Chain B: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 Ligands: WOY.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Y.345 Hydrogen bonds: B:Q.247, B:G.250, B:Y.345 Water bridges: B:V.294 Salt bridges: B:H.237, B:H.237, B:H.252, B:K.292, B:K.292 CIT.5: 11 residues within 4Å: Chain C: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345, L.348 Ligands: WOY.6 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Y.345 Hydrogen bonds: C:Q.247, C:G.250, C:Y.345 Water bridges: C:V.294 Salt bridges: C:H.237, C:H.237, C:H.252, C:K.292, C:K.292 CIT.8: 10 residues within 4Å: Chain D: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 Ligands: WOY.7 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:Y.345 Hydrogen bonds: D:Q.247, D:G.250, D:K.292, D:T.343 Salt bridges: D:H.237, D:H.237, D:H.252, D:K.292, D:K.292, D:K.292 CIT.10: 10 residues within 4Å: Chain E: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 Ligands: WOY.9 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:Y.345 Hydrogen bonds: E:Q.247, E:G.250, E:K.292, E:T.343 Salt bridges: E:H.237, E:H.237, E:H.252, E:K.292, E:K.292, E:K.292 CIT.12: 10 residues within 4Å: Chain F: H.237, Q.247, L.248, G.249, G.250, H.252, K.292, T.343, Y.345 Ligands: WOY.11 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:Y.345 Hydrogen bonds: F:Q.247, F:G.250, F:K.292, F:T.343 Salt bridges: F:H.237, F:H.237, F:H.252, F:K.292, F:K.292, F:K.292

6 x WOY: 6,7-dihydro-5H-pyrrolo[2,3-d]pyrimidine(Non-covalent)

WOY.2: 5 residues within 4Å: Chain A: W.335, E.342, T.343, Y.345 Ligands: CIT.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.343 Hydrogen bonds: A:Y.345 pi-Stacking: A:W.335 WOY.4: 5 residues within 4Å: Chain B: W.335, E.342, T.343, Y.345 Ligands: CIT.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.343 Hydrogen bonds: B:Y.345 pi-Stacking: B:W.335 WOY.6: 5 residues within 4Å: Chain C: W.335, E.342, T.343, Y.345 Ligands: CIT.5 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.343 Hydrogen bonds: C:Y.345 pi-Stacking: C:W.335 WOY.7: 5 residues within 4Å: Chain D: W.335, E.342, T.343, Y.345 Ligands: CIT.8 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.343 pi-Stacking: D:W.335, D:W.335, D:W.335, D:W.335 WOY.9: 5 residues within 4Å: Chain E: W.335, E.342, T.343, Y.345 Ligands: CIT.10 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:T.343 pi-Stacking: E:W.335, E:W.335, E:W.335, E:W.335 WOY.11: 5 residues within 4Å: Chain F: W.335, E.342, T.343, Y.345 Ligands: CIT.12 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:T.343 pi-Stacking: F:W.335, F:W.335, F:W.335, F:W.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Godoy, A.S. et al., Allosteric regulation and crystallographic fragment screening of SARS-CoV-2 NSP15 endoribonuclease. Nucleic Acids Res. (2023)

Release Date

2021-06-09

Peptides

Uridylate-specific endoribonuclease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
B

E
B

F
B

Uridylate-specific endoribonuclease

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