SMTL ID : 6wks.1

Structure of SARS-CoV-2 nsp16/nsp10 in complex with RNA cap analogue (m7GpppA) and S-adenosylmethionine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

SAM.1: 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: GTA.3 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:G.71, A:G.73, A:G.81, A:L.100, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:S.74, A:N.101, A:N.101 Salt bridges: A:D.130

1 x ADN: ADENOSINE(Non-covalent)

ADN.2: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.58, A:T.58 Water bridges: A:N.13, A:T.58

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.3: 18 residues within 4Å: Chain A: C.25, D.26, L.27, Y.30, K.46, Y.132, P.134, K.137, K.170, T.172, E.173, H.174, S.175, N.198, S.201, S.202, E.203 Ligands: SAM.1 25 PLIP interactions: 25 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:Y.30, A:K.46, A:K.46, A:Y.132, A:Y.132, A:K.170, A:T.172, A:H.174, A:S.175, A:N.198, A:S.201, A:S.202 Water bridges: A:N.43, A:N.198, A:N.198, A:S.201 Salt bridges: A:K.137, A:K.137, A:K.137 pi-Stacking: A:Y.30, A:Y.30, A:Y.132 pi-Cation interactions: A:Y.30

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.5: 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

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

EDO.6: 5 residues within 4Å: Chain B: I.38, T.39, N.40, C.41, A.104 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.38, B:C.41, B:A.104 Water bridges: B:N.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Viswanathan, T. et al., Structural basis of RNA cap modification by SARS-CoV-2. Nat Commun (2020)

Release Date

2020-05-06

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

B
BBB

2'-O-methyltransferase

Non-structural protein 10

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