SMTL ID : 7mc5.1

Crystal structure of the SARS-CoV-2 ExoN-nsp10 complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.64 Å

Oligo State

hetero-1-1-mer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.205, C.208, C.224, H.227 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.208, A:C.224, A:H.227 ZN.2: 4 residues within 4Å: Chain A: H.255, C.259, H.262, C.277 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.255, A:C.259, A:H.262, A:C.277 ZN.22: 4 residues within 4Å: Chain B: C.75, C.78, H.84, C.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.23: 4 residues within 4Å: Chain B: C.118, C.121, C.129, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.118, B:C.121, B:C.129, B:C.131

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

EDO.3: 6 residues within 4Å: Chain A: Y.62, Q.63 Chain B: Y.31, S.34, G.35, G.36 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: V.12, T.14, G.15, D.46, Y.49, R.51 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: M.60, Y.62, M.70, F.71 Ligands: EDO.17 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: R.74, W.245, E.282, C.283 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: F.71, H.186, Q.244 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: H.262, R.276, C.277, H.281 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: H.93, G.100, T.101, N.102 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.248, S.253, N.254, L.257 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: H.80, R.82, S.176 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: E.90, H.266, V.267, D.271 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.50, V.123, S.132, R.133, V.134 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain A: Q.20, K.45, M.47, P.126, N.127 Chain B: K.94, G.95 Ligand excluded by PLIP EDO.17: 7 residues within 4Å: Chain A: Y.62, Q.63, V.64, Y.67, P.68, N.69 Ligands: EDO.5 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: S.216, S.219, I.229, G.230, F.231 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: H.262, G.263, C.270, I.273 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: S.10, K.11, V.12 Chain B: N.4 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: T.57, V.58 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: L.36 Chain B: K.44, M.45, L.46, C.47, H.49, E.67 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: H.84, P.85, N.86, F.90, C.91, D.92 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain B: D.92, T.112, N.115, W.124 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: N.65, P.201 Chain B: K.26, D.30 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain B: I.39, T.40, N.41, C.42, N.106, P.108 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: T.48, T.50, G.51, T.59, P.60, E.61 Ligand excluded by PLIP

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.14: 4 residues within 4Å: Chain A: K.11, T.95, R.96, K.137 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.11, A:K.11, A:R.96 Water bridges: A:T.95 Salt bridges: A:K.11, A:K.137, A:K.137 TLA.15: 6 residues within 4Å: Chain A: T.3, G.4, L.5, M.56, G.57, K.59 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.4, A:M.56, A:M.56 Water bridges: A:V.2, A:T.3, A:K.7 Salt bridges: A:K.59

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.20: 1 residues within 4Å: Chain A: E.202 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moeller, N.H. et al., Structure and dynamics of SARS-CoV-2 proofreading exoribonuclease ExoN. Proc.Natl.Acad.Sci.USA (2022)

Release Date

2021-05-05

Peptides

Proofreading exoribonuclease: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
M

Proofreading exoribonuclease

Non-structural protein 10

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