SMTL ID : 6wkq.1 (1 other biounit)

1.98 Angstrom Resolution Crystal Structure of NSP16-NSP10 Heterodimer from SARS-CoV-2 in Complex with Sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.98 Å

Oligo State

hetero-1-1-mer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: R.89, Q.90, L.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.92 NA.2: 3 residues within 4Å: Chain A: I.115, S.295, D.296 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.295, A:D.296 Water bridges: A:I.115

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.3: 18 residues within 4Å: Chain A: N.46, Y.50, G.74, G.76, S.77, P.83, G.84, D.102, L.103, N.104, G.116, D.117, C.118, D.133, M.134, Y.135, F.152 Ligands: FMT.4 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:N.46, A:G.74, A:G.76, A:G.84, A:L.103, A:D.117, A:C.118, A:D.133, A:Y.135 Water bridges: A:G.74, A:A.75, A:S.77, A:D.102, A:N.104, A:N.104, A:K.173, A:K.173

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

FMT.4: 2 residues within 4Å: Chain A: N.46 Ligands: SFG.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.46 Water bridges: A:K.49 FMT.5: 7 residues within 4Å: Chain A: Y.135, T.139, T.175, E.176, H.177, S.205 Ligands: FMT.6 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.135, A:T.175, A:E.176, A:H.177, A:S.205 Water bridges: A:E.176, A:S.205 FMT.6: 3 residues within 4Å: Chain A: S.204, S.205 Ligands: FMT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:K.140, A:S.205 FMT.7: 5 residues within 4Å: Chain A: K.19, W.193, R.219, E.220, I.222 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.219, A:R.219 FMT.8: 5 residues within 4Å: Chain A: V.121, H.122, T.123, Y.155, K.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.123, A:T.123 FMT.9: 6 residues within 4Å: Chain A: R.69, N.125, K.126, E.287, N.288, N.289 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.69, A:R.69, A:N.125, A:K.126, A:N.289 Water bridges: A:E.287, A:N.289

2 x ZN: ZINC ION(Non-covalent)

ZN.10: 4 residues within 4Å: Chain B: C.77, C.80, H.86, C.93 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.77, B:C.80, B:H.86, B:C.93 ZN.11: 4 residues within 4Å: Chain B: C.120, C.123, C.131, C.133 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.120, B:C.123, B:C.131, B:C.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rosas-Lemus, M. et al., High-resolution structures of the SARS-CoV-2 2'- O -methyltransferase reveal strategies for structure-based inhibitor design. Sci.Signal. (2020)

Release Date

2020-04-29

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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