SMTL ID : 7jyy.2 (1 other biounit)

Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

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

M7G-A-U-U-A.1: 28 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, Y.134, P.136, K.139, V.141, K.172, T.174, E.175, H.176, S.177, N.200, S.203, S.204, E.205 Ligands: SAM.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:K.26, A:L.29, A:Y.32, A:K.139, A:T.174, A:T.174, A:E.175, A:H.176, A:S.177, A:S.204 Water bridges: A:D.28, A:D.28 Salt bridges: A:K.139, A:K.139, A:H.176 pi-Stacking: A:Y.32, A:Y.32 pi-Cation interactions: A:Y.32

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.2: 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-A-U-U-A.1, M7G-A-U-U-A.1 17 PLIP interactions: 17 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:D.116, A:D.116, A:C.117, A:D.132, A:Y.134 Water bridges: A:G.73, A:D.101, A:N.103, A:N.103, A:F.151 Salt bridges: A:D.132

1 x MG: MAGNESIUM ION(Non-covalent)

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

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: N.57, K.251, F.252, P.253 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.251 Water bridges: A:K.255 NA.5: 4 residues within 4Å: Chain A: R.88, Q.89, L.91 Chain B: T.60 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.60, A:L.91

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

FMT.6: 6 residues within 4Å: Chain A: R.68, N.124, K.125, E.286, N.287, N.288 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.68, A:R.68, A:N.124, A:K.125, A:N.288, A:N.288 Water bridges: A:E.286 FMT.7: 4 residues within 4Å: Chain A: A.123, K.125, Q.161, K.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.125, A:K.162 FMT.8: 5 residues within 4Å: Chain A: V.120, H.121, T.122, Y.154, K.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.122, A:Y.154, A:Y.154

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 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.10: 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

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

2020-09-16

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

2'-O-methyltransferase

Non-structural protein 10

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