SMTL ID : 6w75.2 (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

5 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: N.58, L.60 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.60 Water bridges: A:L.62, A:L.62 NA.3: 2 residues within 4Å: Chain A: Q.161, Y.214 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.214 Water bridges: A:Y.214 NA.4: 3 residues within 4Å: Chain A: I.115, S.295, D.296 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.295, A:D.296 NA.18: 2 residues within 4Å: Chain B: T.114, N.117 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.117 Water bridges: B:V.119

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

SAM.5: 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:N.104, A:D.117, A:D.117, A:C.118, A:D.133, A:Y.135 Water bridges: A:G.74, A:D.102, A:F.152 Salt bridges: A:D.133

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

FMT.6: 6 residues within 4Å: Chain A: R.69, N.125, K.126, E.287, N.288, N.289 8 PLIP interactions: 8 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:A.124, A:E.287 FMT.7: 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:T.175, A:E.176, A:H.177, A:S.205 Water bridges: A:E.176, A:E.176 FMT.8: 5 residues within 4Å: Chain A: K.173, N.201, S.204, E.206 Ligands: FMT.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.201, A:S.204 Water bridges: A:K.49, A:K.49, A:K.173 FMT.9: 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.10: 4 residues within 4Å: Chain A: S.204, S.205 Ligands: FMT.7, FMT.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.205 Water bridges: A:E.176, A:E.176, A:S.205 FMT.11: 6 residues within 4Å: Chain A: A.37, T.38, L.242, S.243, S.244, Y.245 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.38, A:T.38, A:S.244, A:Y.245 FMT.12: 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.13: 5 residues within 4Å: Chain A: V.121, H.122, T.123, Y.155, K.163 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.123, A:Y.155, A:Y.155 FMT.14: 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:A.124, A:K.126 FMT.15: 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.19: 3 residues within 4Å: Chain A: G.42 Chain B: K.46, A.107 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.46

2 x ZN: ZINC ION(Non-covalent)

ZN.16: 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.17: 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
C

B
D

2'-O-methyltransferase

Non-structural protein 10

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