SMTL ID : 6xdh.1 (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

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

ACT.1: 5 residues within 4Å: Chain A: N.95, G.98, V.99, D.100 Chain C: D.58 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:D.58 ACT.5: 5 residues within 4Å: Chain A: D.58 Chain B: N.95, G.98, V.99, D.100 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.58 ACT.9: 5 residues within 4Å: Chain B: D.58 Chain C: N.95, G.98, V.99, D.100 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:D.58

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

CIT.2: 10 residues within 4Å: Chain A: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364, L.367 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.266, A:G.269 Salt bridges: A:H.256, A:H.256, A:H.271, A:K.311, A:K.311 CIT.6: 10 residues within 4Å: Chain B: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364, L.367 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Q.266, B:G.269 Salt bridges: B:H.256, B:H.256, B:H.271, B:K.311, B:K.311 CIT.10: 10 residues within 4Å: Chain C: H.256, Q.266, L.267, G.268, G.269, H.271, K.311, T.362, Y.364, L.367 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:Q.266, C:G.269 Salt bridges: C:H.256, C:H.256, C:H.271, C:K.311, C:K.311

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

FMT.3: 3 residues within 4Å: Chain A: S.265, Q.266, S.310 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.265 FMT.4: 8 residues within 4Å: Chain A: L.333, S.334, V.335, V.336, C.355, K.356, D.357, G.358 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.355, A:D.357, A:G.358 FMT.7: 3 residues within 4Å: Chain B: S.265, Q.266, S.310 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.265 FMT.8: 8 residues within 4Å: Chain B: L.333, S.334, V.335, V.336, C.355, K.356, D.357, G.358 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.355, B:D.357, B:G.358 FMT.11: 3 residues within 4Å: Chain C: S.265, Q.266, S.310 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.265 FMT.12: 8 residues within 4Å: Chain C: L.333, S.334, V.335, V.336, C.355, K.356, D.357, G.358 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:C.355, C:D.357, C:G.358

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
A

B
A

C
A

Uridylate-specific endoribonuclease

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