SMTL ID : 8s8w.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

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

U-U-A.1: 14 residues within 4Å: Chain A: S.33, A.34, T.35, L.36, M.41, M.42, N.43, K.46, S.74, D.75, K.76, N.198 Ligands: SAM.3, GTA.10 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 SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.3: 25 residues within 4Å: Chain A: N.43, Y.47, H.69, G.71, A.72, G.73, S.74, P.80, G.81, 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: U-U-A.1, SGV.4, GTA.10 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:Y.47, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71 Salt bridges: A:D.130

1 x SGV: SANGIVAMYCIN(Non-covalent)

SGV.4: 17 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, K.135, F.149 Ligands: SAM.3, GTA.10 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:G.73, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:D.130, A:Y.132, A:D.133 Water bridges: A:G.71

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.5: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.158, A:D.179 EDO.6: 8 residues within 4Å: Chain A: R.66, A.121, N.122, K.123, R.283, E.284, N.285, N.286 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.66, A:R.66, A:K.123, A:K.123, A:E.284, A:E.284, A:N.286 EDO.7: 7 residues within 4Å: Chain A: K.16, M.17, W.190, R.216, E.217, I.219, M.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.190, A:E.217

2 x ZN: ZINC ION(Non-covalent)

ZN.8: 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.9: 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.10: 24 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-A.1, SAM.3, SGV.4 30 PLIP interactions: 30 interactions with chain A Hydrogen bonds: A:K.24, A:L.27, A:Y.30, A:Y.30, A:K.46, A:D.130, A:K.137, A:K.170, A:T.172, A:T.172, A:E.173, A:H.174, A:H.174, A:S.175, A:S.202, A:S.202, A:E.203 Water bridges: A:Y.30, A:N.43, A:S.201, A:S.201, A:S.201 Salt bridges: A:D.26, A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.132 pi-Cation interactions: A:Y.30

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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