SMTL ID : 9eun.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with SAM and m7GTP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

Ligands

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

MES.1: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:T.58, A:W.189

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

SAM.2: 22 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, F.149, K.170 Ligands: EDO.6 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:G.73, A:G.73, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:D.130, A:Y.132 Water bridges: A:G.71 Salt bridges: A:D.130

1 x MGP: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

MGP.3: 16 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Y.30, Y.132, T.136, K.137, V.139, T.172, E.173, H.174, S.175, S.201, S.202, E.203 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:D.26, A:L.27, A:Y.30, A:Y.132, A:H.174, A:H.174, A:S.175, A:S.201, A:S.202, A:S.202 Water bridges: A:K.24 Salt bridges: A:K.137, A:K.137, A:K.137, A:H.174 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24, A:Y.30

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

EDO.4: 6 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, I.219, M.224 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.190, A:E.217 EDO.5: 6 residues within 4Å: Chain A: A.34, T.35, L.239, S.240, S.241, Y.242 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.35, A:S.241, A:S.241 Water bridges: A:L.239, A:Y.242 EDO.6: 5 residues within 4Å: Chain A: N.43, S.74, D.75, K.76 Ligands: SAM.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.75 EDO.7: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.44 EDO.8: 5 residues within 4Å: Chain A: Q.6, P.7, Q.52, S.243, D.246 No protein-ligand interaction detected (PLIP) EDO.9: 9 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93, L.254 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.64, A:N.64, A:M.65, A:T.93 EDO.10: 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:Q.158, A:K.182 EDO.11: 3 residues within 4Å: Chain A: L.22, E.23, K.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.24 EDO.12: 5 residues within 4Å: Chain A: A.116, T.117, H.119, D.293, L.295 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.116, A:D.293 EDO.15: 10 residues within 4Å: Chain A: M.41 Chain B: I.39, T.40, N.41, C.42, F.69, A.105, N.106, P.108 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.41, B:C.42, B:C.42 Water bridges: B:K.44 EDO.16: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.92, B:N.115

2 x ZN: ZINC ION(Non-covalent)

ZN.13: 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.14: 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 development. To Be Published

Release Date

2024-05-01

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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