SMTL ID : 8s8x.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with Toyocamycin and m7GpppA-RNA (Cap0-RNA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

hetero-1-1-mer

Ligands

1 x U- U: m7GpppA-RNA (Cap0-RNA)(Non-covalent)

U-U.1: 10 residues within 4Å: Chain A: M.41, M.42, N.43, K.46, S.74, D.75, K.76, N.198 Ligands: MG.4, GTA.7 Protein-ligand interaction information (PLIP) not available

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x TO1: 4-amino-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidine-5-carbonitrile(Non-covalent)

TO1.3: 16 residues within 4Å: Chain A: G.71, G.73, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, D.133, P.134, F.149, K.170 Ligands: GTA.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:K.135, A:F.149

1 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: N.198, S.201 Ligands: U-U.1 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain B: C.75, Y.77, C.78, H.84, C.91 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.6: 5 residues within 4Å: Chain B: C.118, V.120, C.121, C.129, C.131 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.118, B:C.121, B:C.129, B:C.131

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.7: 23 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.46, D.130, Y.132, P.134, T.136, K.137, V.139, K.170, T.172, E.173, H.174, S.175, N.198, S.201, S.202, E.203 Ligands: U-U.1, TO1.3 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:K.24, A:L.27, A:Y.30, A:K.46, A:K.137, A:K.170, A:T.172, A:E.173, A:H.174, A:S.175, A:S.202, A:S.202, A:E.203 Water bridges: A:D.130, A:D.130, A:N.198, A:S.201 Salt bridges: A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.132 pi-Cation interactions: A:K.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kremling, V. et al., SARS-CoV-2 methyltransferase nsp10-16 in complex with natural and drug-like purine analogs for guiding structure-based drug discovery. Elife (2024)

Release Date

2024-03-20

Peptides

2'-O-methyltransferase nsp16: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

2'-O-methyltransferase nsp16

Non-structural protein 10

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