SMTL ID : 6wkq.2 (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: 4 residues within 4Å: Chain A: R.89, Q.90, W.91, L.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.92 NA.2: 2 residues within 4Å: Chain A: I.115, S.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.295, A:S.295 Water bridges: A:I.115

1 x SFG: SINEFUNGIN(Non-covalent)

SFG.3: 19 residues within 4Å: Chain A: N.46, Y.50, G.74, A.75, 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.12 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:N.46, A:Y.50, A:Y.50, A:G.74, A:G.76, A:G.84, A:L.103, A:D.117, A:D.117, A:C.118, A:D.133, A:Y.135 Water bridges: A:G.74, A:D.102, A:N.104, A:N.104, A:D.133, A:D.133, A:F.152, A:K.173, A:K.173

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

FMT.4: 6 residues within 4Å: Chain A: Y.135, T.175, E.176, H.177, S.205 Ligands: FMT.10 6 PLIP interactions: 6 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 FMT.5: 5 residues within 4Å: Chain A: K.149, E.150, G.151, F.152, F.153 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.151, A:G.151, A:F.153 Water bridges: A:F.152 FMT.6: 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 FMT.7: 4 residues within 4Å: Chain A: A.124, K.126, Q.162, K.163 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.126, A:K.163 Water bridges: A:K.126, A:Q.162 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:H.122, A:T.123 FMT.9: 2 residues within 4Å: Chain A: P.15, N.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.16, A:N.16 FMT.10: 3 residues within 4Å: Chain A: S.204, S.205 Ligands: FMT.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:E.176, A:S.205, A:S.205, A:S.205 FMT.11: 6 residues within 4Å: Chain A: A.37, T.38, L.242, S.243, S.244, Y.245 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.38, A:T.38, A:S.244 FMT.12: 2 residues within 4Å: Chain A: N.46 Ligands: SFG.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.46 Water bridges: A:N.46, A:K.49, A:K.49, A:K.49, A:D.133, A:D.133, A:D.133

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 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.14: 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
C

B
D

2'-O-methyltransferase

Non-structural protein 10

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