SMTL ID : 6wjt.1 (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: 3 residues within 4Å: Chain A: R.89, Q.90, L.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.89

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 12 PLIP interactions: 12 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:Y.135 Water bridges: A:G.74, A:G.76, A:N.104, A:N.104

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

FMT.3: 7 residues within 4Å: Chain A: Y.135, T.139, T.175, E.176, H.177, S.205 Ligands: FMT.4 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.4: 3 residues within 4Å: Chain A: S.204, S.205 Ligands: FMT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:S.205, A:S.205 FMT.5: 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.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: N.58, P.254, L.255, K.256 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.256 Water bridges: A:N.58, A:N.58, A:L.60, A:L.60 FMT.8: 5 residues within 4Å: Chain A: S.148, E.150, N.180, A.181, D.182 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.148, A:E.150, A:N.180, A:A.181, A:D.182, A:D.182 FMT.9: 4 residues within 4Å: Chain A: A.124, N.125, Q.162, K.163 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.163 Water bridges: A:K.126 FMT.12: 6 residues within 4Å: Chain A: I.43 Chain B: K.46, M.47, L.48, C.49, H.51 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.49 Water bridges: B:K.46, B:K.46

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

2020-04-22

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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