SMTL ID : 7keh.1

Crystal structure from SARS-CoV-2 NendoU NSP15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.59 Å

Oligo State

homo-hexamer

Ligands

6 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.1: 5 residues within 4Å: Chain A: F.46, E.47, W.61, W.89, D.94 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:E.47, A:E.47, C:E.269 Water bridges: A:E.47, A:D.94, A:D.94, A:D.94, A:D.94 B3P.3: 5 residues within 4Å: Chain B: F.46, E.47, W.61, W.89, D.94 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.47, B:E.47, A:E.269 Water bridges: B:E.47, B:D.94, B:D.94, B:D.94, B:D.94 B3P.5: 5 residues within 4Å: Chain C: F.46, E.47, W.61, W.89, D.94 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:E.47, C:E.47, B:E.269 Water bridges: C:E.47, C:D.94, C:D.94, C:D.94, C:D.94 B3P.7: 6 residues within 4Å: Chain D: F.46, E.47, W.61, W.89, D.94 Chain E: E.269 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:E.47, D:E.47, E:E.269, E:E.269 Water bridges: D:E.47, D:D.94 B3P.9: 6 residues within 4Å: Chain E: F.46, E.47, W.61, W.89, D.94 Chain F: E.269 6 PLIP interactions: 4 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:E.47, E:E.47, F:E.269, F:E.269 Water bridges: E:E.47, E:D.94 B3P.11: 6 residues within 4Å: Chain D: E.269 Chain F: F.46, E.47, W.61, W.89, D.94 6 PLIP interactions: 4 interactions with chain F, 2 interactions with chain D Hydrogen bonds: F:E.47, F:E.47, D:E.269, D:E.269 Water bridges: F:E.47, F:D.94

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 7 residues within 4Å: Chain A: H.237, G.249, G.250, H.252, K.292, T.343, Y.345 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.250, A:T.343 Salt bridges: A:H.237, A:H.252, A:K.292 SO4.4: 7 residues within 4Å: Chain B: H.237, G.249, G.250, H.252, K.292, T.343, Y.345 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.250, B:T.343 Salt bridges: B:H.237, B:H.252, B:K.292 SO4.6: 7 residues within 4Å: Chain C: H.237, G.249, G.250, H.252, K.292, T.343, Y.345 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.250, C:T.343 Salt bridges: C:H.237, C:H.252, C:K.292 SO4.8: 6 residues within 4Å: Chain D: H.237, G.249, G.250, H.252, K.292, T.343 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.250 Salt bridges: D:H.237, D:H.252, D:K.292 SO4.10: 6 residues within 4Å: Chain E: H.237, G.249, G.250, H.252, K.292, T.343 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.250 Salt bridges: E:H.237, E:H.252, E:K.292 SO4.12: 6 residues within 4Å: Chain F: H.237, G.249, G.250, H.252, K.292, T.343 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:G.250 Salt bridges: F:H.237, F:H.252, F:K.292

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

2020-12-02

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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