SMTL ID : 7lw4.1

Structure of SARS-CoV-2 nsp16/nsp10 complex in presence of S-adenosyl-L-homocysteine (SAH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-mer

Ligands

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

MES.1: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

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

ACT.2: 7 residues within 4Å: Chain A: Y.132, T.136, K.137, T.172, E.173, H.174, S.202 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.137 Hydrogen bonds: A:E.173, A:H.174 Water bridges: A:S.202, A:S.202 Salt bridges: A:H.174 ACT.3: 7 residues within 4Å: Chain A: K.46, K.170, T.172, N.198, S.201, E.203 Ligands: EDO.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.203 Water bridges: A:K.170 Salt bridges: A:K.46, A:K.170 ACT.6: 5 residues within 4Å: Chain A: R.19, I.219, D.220, V.223, M.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.220 ACT.8: 7 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.149 Hydrogen bonds: A:F.149 ACT.9: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.291 ACT.10: 4 residues within 4Å: Chain A: K.182, H.186, P.215, Q.218 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.215 Hydrogen bonds: A:Q.218 Water bridges: A:I.219 Salt bridges: A:K.182, A:H.186 ACT.11: 6 residues within 4Å: Chain A: A.34, T.35, L.239, S.240, S.241, Y.242 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.241 ACT.13: 2 residues within 4Å: Chain A: I.40, M.41 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:M.41 Hydrogen bonds: A:I.40 Water bridges: A:I.40 ACT.16: 5 residues within 4Å: Chain B: I.38, T.39, N.40, C.41, P.107 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.40, B:C.41

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

EDO.4: 5 residues within 4Å: Chain A: M.42, N.43, K.46, N.198 Ligands: ACT.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.43, A:N.43, A:K.46, A:N.198 Water bridges: A:N.198 EDO.5: 5 residues within 4Å: Chain A: D.114, A.116, G.148, F.149 Ligands: SAH.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.114 EDO.7: 6 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, I.219, M.224 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.190

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

SAH.12: 19 residues within 4Å: Chain A: N.43, Y.47, G.71, A.72, G.73, S.74, P.80, G.81, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, F.149 Ligands: EDO.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.81, A:L.100, A:N.101, A:D.114, A:D.114, A:C.115, A:D.130, A:Y.132 Water bridges: A:G.71, A:A.72, A:D.99

2 x ZN: ZINC ION(Non-covalent)

ZN.14: 5 residues within 4Å: Chain B: C.74, Y.76, 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.15: 5 residues within 4Å: Chain B: C.117, V.119, 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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