SMTL ID : 6wjt.2 (1 other biounit)

2.0 Angstrom Resolution Crystal Structure of Nsp16-Nsp10 Heterodimer from SARS-CoV-2 in Complex with S-Adenosyl-L-Homocysteine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-1-1-mer

Ligands

1 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

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

SAH.2: 18 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 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:N.46, 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:G.76, A:N.104, A:N.104, A:F.152

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

FMT.3: 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, A:N.289 Water bridges: A:E.287 FMT.4: 6 residues within 4Å: Chain A: Y.135, T.139, T.175, E.176, H.177, S.205 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.175, A:E.176, A:H.177, A:S.205, A:S.205 Water bridges: A:E.176 FMT.5: 2 residues within 4Å: Chain A: P.15, N.16 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.16, A:N.16 Water bridges: A:N.16, A:L.17 FMT.6: 4 residues within 4Å: Chain A: A.124, K.126, Q.162, K.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.126, A:K.163 FMT.7: 5 residues within 4Å: Chain A: I.115, G.116, T.120, S.295, D.296 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.120, A:S.295 Water bridges: A:I.115, A:D.117

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 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

2020-04-22

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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