SMTL ID : 7l6t.1

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA2m)pUpUpApApA (Cap-1), S-Adenosyl-L-homocysteine (SAH) and two Magnesium (Mg) ions.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

hetero-1-1-mer

Ligands

1 x M7G- A2M- U- U- A: RNA (5'-D(*(M7G))-R(P*(A2M)P*UP*UP*A)-3')(Non-covalent)

M7G-A2M-U-U-A.1: 30 residues within 4Å: Chain A: K.26, C.27, D.28, L.29, Y.32, S.35, A.36, L.38, M.44, N.45, K.48, S.76, D.77, K.78, D.132, Y.134, P.136, K.139, K.172, T.174, E.175, H.176, S.177, N.200, S.203, S.204, E.205 Ligands: SAH.5, GLC.6, MG.11 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:K.48, A:K.172, A:K.26, A:L.29, A:Y.32, A:Y.134, A:K.139, A:T.174, A:H.176, A:S.177, A:S.204 Water bridges: A:N.45, A:K.139, A:K.139, A:N.200, A:N.200, A:K.26, A:D.28, A:D.28 Salt bridges: A:K.139, A:K.139, A:K.139 pi-Stacking: A:Y.134, A:Y.32, A:Y.32 pi-Cation interactions: A:Y.32

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: N.200 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain A: K.78 Ligands: M7G-A2M-U-U-A.1, M7G-A2M-U-U-A.1 No protein-ligand interaction detected (PLIP)

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

CL.3: 3 residues within 4Å: Chain A: L.59, T.60, C.211 Ligand excluded by PLIP

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

FMT.4: 6 residues within 4Å: Chain A: R.68, N.124, K.125, E.286, N.287, N.288 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:K.125, A:E.286, A:N.288

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

SAH.5: 20 residues within 4Å: Chain A: N.45, Y.49, G.73, A.74, G.75, S.76, P.82, G.83, D.101, L.102, N.103, G.115, D.116, C.117, D.132, M.133, Y.134, F.151 Ligands: M7G-A2M-U-U-A.1, GLC.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.45, A:Y.49, A:G.73, A:G.75, A:G.83, A:L.102, A:N.103, A:D.116, A:C.117, A:Y.134 Water bridges: A:G.73, A:S.76, A:F.151

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.6: 8 residues within 4Å: Chain A: S.76, D.77, D.101, N.103, P.136 Ligands: M7G-A2M-U-U-A.1, M7G-A2M-U-U-A.1, SAH.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.103 Water bridges: A:S.76, A:S.76, A:D.77 GLC.7: 6 residues within 4Å: Chain A: S.35, A.36, T.37, S.242, S.243, Y.244 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.35, A:T.37, A:S.243, A:S.243, A:S.243 Water bridges: A:Q.240

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 4 residues within 4Å: Chain B: C.76, C.79, H.85, C.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.76, B:C.79, B:H.85, B:C.92 ZN.9: 4 residues within 4Å: Chain B: C.119, C.122, C.130, C.132 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.119, B:C.122, B:C.130, B:C.132

1 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.10: 7 residues within 4Å: Chain A: M.43 Chain B: I.40, T.41, N.42, C.43, F.70, P.109 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:I.40, B:N.42, B:N.42, B:C.43, B:C.43 Water bridges: B:K.45, B:A.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Mn 2+ coordinates Cap-0-RNA to align substrates for efficient 2'- O -methyl transfer by SARS-CoV-2 nsp16. Sci.Signal. (2021)

Release Date

2021-01-06

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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