SMTL ID : 9emv.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with Sangivamycin and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.34 Å

Oligo State

hetero-1-1-mer

Ligands

1 x SGV: SANGIVAMYCIN(Non-covalent)

SGV.1: 18 residues within 4Å: Chain A: G.71, G.73, S.74, S.98, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, D.133, F.149 Ligands: GTA.2, SAH.4, V9G.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:D.99, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:D.130, A:Y.132

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

GTA.2: 23 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, K.46, 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: SGV.1, SAH.4, V9G.11 22 PLIP interactions: 22 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:K.46, A:Y.132, A:K.137, A:K.170, A:H.174, A:H.174, A:S.175, A:N.198, A:S.201, A:S.202, A:S.202 Water bridges: A:N.43, A:N.43 Salt bridges: A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.30, A:Y.132

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

MES.3: 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 SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 24 residues within 4Å: Chain A: N.43, Y.47, H.69, G.71, A.72, G.73, S.74, P.80, G.81, S.98, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, D.133, F.149 Ligands: SGV.1, GTA.2, V9G.11 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:Y.47, A:G.71, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132

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

EDO.5: 3 residues within 4Å: Chain A: Q.28, N.29, D.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.32 EDO.6: 7 residues within 4Å: Chain A: F.150, T.151, C.154, G.155, Q.158, D.179 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.179, A:D.179 EDO.7: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.159 Water bridges: A:Q.159 EDO.8: 5 residues within 4Å: Chain A: Q.158, D.179, K.182, L.183, H.186 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.158, A:D.179, A:K.182 EDO.9: 6 residues within 4Å: Chain A: L.36, P.37, K.38, G.39, I.40, M.41 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.39, A:I.40, A:I.40 EDO.10: 5 residues within 4Å: Chain A: W.5, P.7, Q.52, S.243, D.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.246 EDO.14: 7 residues within 4Å: Chain B: T.112, L.113, K.114, N.115, T.116, V.117, W.124 No protein-ligand interaction detected (PLIP) EDO.15: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, T.102, A.105, N.106 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.44

1 x V9G: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE(Non-covalent)

V9G.11: 25 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, N.43, 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: SGV.1, GTA.2, SAH.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:K.46, A:Y.132, A:K.170, A:H.174, A:H.174, A:S.175, A:N.198, A:S.201, A:S.201, A:S.202, A:S.202 Water bridges: A:N.43, A:N.43 Salt bridges: A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.30

2 x ZN: ZINC ION(Non-covalent)

ZN.12: 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.13: 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

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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