SMTL ID : 6xdh.2 (1 other biounit)

Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-trimer

Ligands

9 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 3 residues within 4Å: Chain A: K.341, V.342, T.343 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.343 Water bridges: A:T.343, A:T.343 FMT.3: 5 residues within 4Å: Chain A: G.147, R.148, T.166, E.167, G.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.167, A:G.168 FMT.7: 3 residues within 4Å: Chain A: E.250, Y.252, G.358 No protein-ligand interaction detected (PLIP) FMT.8: 3 residues within 4Å: Chain B: K.341, V.342, T.343 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.343 Water bridges: B:T.343, B:T.343 FMT.10: 5 residues within 4Å: Chain B: G.147, R.148, T.166, E.167, G.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.167, B:G.168 FMT.14: 3 residues within 4Å: Chain B: E.250, Y.252, G.358 No protein-ligand interaction detected (PLIP) FMT.15: 3 residues within 4Å: Chain C: K.341, V.342, T.343 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.343 Water bridges: C:T.343, C:T.343 FMT.17: 5 residues within 4Å: Chain C: G.147, R.148, T.166, E.167, G.168 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.167, C:G.168 FMT.21: 3 residues within 4Å: Chain C: E.250, Y.252, G.358 No protein-ligand interaction detected (PLIP)

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 5 residues within 4Å: Chain A: N.95, G.98, V.99, D.100 Chain B: D.58 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.58 Water bridges: A:V.99 ACT.5: 3 residues within 4Å: Chain A: M.231, Y.247, K.329 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.247 Salt bridges: A:K.329 ACT.9: 5 residues within 4Å: Chain B: N.95, G.98, V.99, D.100 Chain C: D.58 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:D.58 Water bridges: B:V.99 ACT.12: 3 residues within 4Å: Chain B: M.231, Y.247, K.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.247 Salt bridges: B:K.329 ACT.16: 5 residues within 4Å: Chain A: D.58 Chain C: N.95, G.98, V.99, D.100 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Water bridges: C:V.99 Hydrogen bonds: A:D.58 ACT.19: 3 residues within 4Å: Chain C: M.231, Y.247, K.329 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.247 Salt bridges: C:K.329

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

CIT.4: 9 residues within 4Å: Chain A: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.364 Hydrogen bonds: A:Q.266, A:G.269, A:T.362 Water bridges: A:H.271, A:V.313 Salt bridges: A:H.256, A:H.256, A:H.271, A:K.311, A:K.311 CIT.11: 9 residues within 4Å: Chain B: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:Y.364 Hydrogen bonds: B:Q.266, B:G.269, B:T.362 Water bridges: B:H.271, B:V.313 Salt bridges: B:H.256, B:H.256, B:H.271, B:K.311, B:K.311 CIT.18: 9 residues within 4Å: Chain C: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:Y.364 Hydrogen bonds: C:Q.266, C:G.269, C:T.362 Water bridges: C:H.271, C:V.313 Salt bridges: C:H.256, C:H.256, C:H.271, C:K.311, C:K.311

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

EDO.6: 3 residues within 4Å: Chain A: F.65, E.66, W.80 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.66 Water bridges: A:E.66, A:W.108, A:D.113, A:D.113 EDO.13: 3 residues within 4Å: Chain B: F.65, E.66, W.80 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.66 Water bridges: B:E.66, B:W.108, B:D.113, B:D.113 EDO.20: 3 residues within 4Å: Chain C: F.65, E.66, W.80 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:E.66 Water bridges: C:E.66, C:W.108, C:D.113, C:D.113

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dranow, D.M. et al., Crystal Structure of NendoU (Uridylate-specific endoribonuclease, nsp15) from Betacoronavirus SARS-CoV-2. to be published

Release Date

2020-06-17

Peptides

Uridylate-specific endoribonuclease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

Uridylate-specific endoribonuclease

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