SMTL ID : 7lw3.1

Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of Cap-1 analog (m7GpppAmU) and SAH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 2 residues within 4Å: Chain A: T.58, W.189 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13, A:T.58 pi-Cation interactions: A:W.189, A:W.189

1 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: N.198 No protein-ligand interaction detected (PLIP)

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.3: 11 residues within 4Å: Chain A: N.43, Y.47, G.71, A.72, G.73, D.99, D.114, D.130, M.131, Y.132 Ligands: YG4.4 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:N.43, A:G.73, A:G.73, A:N.101, A:D.114, A:Y.132 Water bridges: A:G.71, A:G.81, A:L.100, A:N.101

1 x YG4: [(2~{R},3~{R},4~{R},5~{R})-5-(6-azanyl-7,8-dihydropurin-9-yl)-2-[[[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-7-methyl-6-oxidanylidene-1,8-dihydropurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-4-methoxy-oxolan-3-yl] [(2~{R},3~{S},4~{R},5~{S})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate(Non-covalent)

YG4.4: 18 residues within 4Å: Chain A: C.25, D.26, L.27, Y.30, N.43, K.46, D.75, D.130, Y.132, K.137, K.170, T.172, E.173, H.174, S.201, S.202, E.203 Ligands: SAH.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:Y.30, A:N.43, A:Y.132, A:K.137, A:K.170, A:T.172, A:E.173, A:H.174, A:S.202 Water bridges: A:D.26, A:L.27, A:N.198, A:N.198, A:N.198 Salt bridges: A:K.46, A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.30, A:Y.132

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

EDO.5: 4 residues within 4Å: Chain B: T.39, N.40, C.41, A.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.38, B:N.40, B:C.41, B:A.104

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain B: C.74, C.77, H.83, C.90 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.74, B:C.77, B:H.83, B:C.90 ZN.7: 4 residues within 4Å: Chain B: C.117, C.120, C.128, C.130 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.117, B:C.120, B:C.128, B:C.130

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, T. et al., A metal ion orients SARS-CoV-2 mRNA to ensure accurate 2'-O methylation of its first nucleotide. Nat Commun (2021)

Release Date

2021-05-05

Peptides

2'-O-methyltransferase: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase

Non-structural protein 10

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