SMTL ID : 7l6r.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

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

M7G-A2M-U-U-A-A.1: 29 residues within 4Å: Chain A: 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: MN.2, SAH.6, GLC.7 16 PLIP interactions: 16 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: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: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

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 2 residues within 4Å: Chain A: N.200 Ligands: M7G-A2M-U-U-A-A.1 No protein-ligand interaction detected (PLIP)

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

CL.3: 4 residues within 4Å: Chain A: N.57, P.253, L.254, K.255 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: K.148, E.149 Ligand excluded by PLIP

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: H.121, T.122, K.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.122, A:T.122 Salt bridges: A:H.121, A:K.162

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

SAH.6: 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-A.1, GLC.7 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.45, A:G.73, A:G.75, A:G.83, A:L.102, A:D.116, A:C.117, A:Y.134 Water bridges: A:G.73, A:A.74, A:N.103, A:F.151

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

GLC.7: 8 residues within 4Å: Chain A: S.76, D.77, D.101, N.103, P.136 Ligands: M7G-A2M-U-U-A-A.1, M7G-A2M-U-U-A-A.1, SAH.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.76, A:N.103 Water bridges: A:S.76 GLC.8: 7 residues within 4Å: Chain A: S.35, A.36, T.37, L.241, S.242, S.243, Y.244 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.35, A:T.37, A:S.243, A:S.243, A:S.243 GLC.9: 5 residues within 4Å: Chain A: L.59, T.60, W.191, N.212, S.278 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.60, A:T.60, A:T.60, A:N.212 Water bridges: A:T.58 GLC.10: 2 residues within 4Å: Chain A: S.4, W.7 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.11: 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

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

BDF.12: 7 residues within 4Å: Chain A: M.43 Chain B: I.40, T.41, N.42, C.43, F.70, P.109 6 PLIP interactions: 6 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

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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