SMTL ID : 6w75.1 (1 other biounit)

1.95 Angstrom Resolution Crystal Structure of NSP10 - NSP16 Complex from SARS-CoV-2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 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.14: 2 residues within 4Å: Chain B: T.105, N.108 No protein-ligand interaction detected (PLIP)

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

SAM.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 14 PLIP interactions: 14 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:S.77, A:D.102, A:N.104, A:F.152 Salt bridges: A:D.133

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

FMT.3: 8 residues within 4Å: Chain A: Y.135, T.139, K.140, T.175, E.176, H.177, S.205 Ligands: FMT.5 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: 5 residues within 4Å: Chain A: K.173, N.201, S.204, E.206 Ligands: FMT.5 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.201, A:S.204, A:S.204, A:E.206 Water bridges: A:K.49, A:K.173 FMT.5: 5 residues within 4Å: Chain A: K.140, S.204, S.205 Ligands: FMT.3, FMT.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.140, A:K.140, A:S.205 Water bridges: A:S.205 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, A:N.289 Water bridges: A:E.287 FMT.7: 3 residues within 4Å: Chain A: M.44, M.45, K.79 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.45, A:K.79, A:K.79 FMT.8: 2 residues within 4Å: Chain A: K.149, E.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.148, A:E.150 FMT.9: 5 residues within 4Å: Chain A: V.121, H.122, T.123, Y.155, K.163 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.123 FMT.10: 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.11: 5 residues within 4Å: Chain A: K.19, W.193, R.219, E.220, I.222 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.219, A:R.219 Water bridges: A:W.193

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 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.13: 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

2020-03-25

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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