SMTL ID : 6w4h.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SO3: SULFITE ION(Non-covalent)

SO3.1: 1 residues within 4Å: Chain A: W.8 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.8

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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:N.46, A:G.74, A:G.76, A:G.84, A:L.103, A:N.104, A:D.117, A:C.118, A:Y.135 Water bridges: A:G.74, A:S.77, A:D.102, A:F.152, A:F.152 Salt bridges: A:D.133

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: K.49, T.175, N.201, S.204, E.206 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:T.175 Hydrogen bonds: A:N.201, A:S.204, A:S.204 Water bridges: A:K.49, A:K.49 Salt bridges: A:K.49, A:K.173 ACT.4: 7 residues within 4Å: Chain A: D.136, T.139, K.149, E.150, G.151, F.152, F.153 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.149, A:F.152, A:F.153 Hydrogen bonds: A:F.152 Water bridges: A:D.136, A:T.139

2 x BDF: beta-D-fructopyranose(Non-covalent)

BDF.5: 4 residues within 4Å: Chain A: L.60, T.61, W.192, C.212 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.61, A:T.61, A:T.61 BDF.8: 7 residues within 4Å: Chain A: M.44 Chain B: I.41, T.42, N.43, C.44, F.71, P.110 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:I.41, B:N.43, B:N.43, B:C.44, B:C.44 Water bridges: B:K.46

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 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.7: 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

2020-03-18

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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