SMTL ID : 8osx.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 18 residues within 4Å: Chain A: G.71, G.73, S.74, D.75, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, P.134, F.149, K.170 Ligands: SAM.15, EDO.21 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:D.75, A:D.75, A:D.75, A:L.100, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:D.99, A:N.101 Salt bridges: A:K.170

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

EDO.2: 7 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: K.24, V.139, K.141, N.143, E.173, H.174 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: S.33, A.34, T.35, S.240, S.241 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: T.35, L.36, K.38 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: T.117, D.293, L.295 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.66, N.122, K.123, E.284, N.285, N.286 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.14 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57 Ligands: MES.3 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.16, M.17, W.190, E.217 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: A.116, Y.152 Ligands: EDO.11 Ligand excluded by PLIP EDO.16: 8 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Y.132, K.137, S.201, S.202 Ligands: EDO.21 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: D.102, F.103, V.104, S.105, T.110 Chain B: K.94 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: N.55, T.56, L.57, R.255 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: Y.132, K.170, N.198, S.201, E.203 Ligands: ATP.1, EDO.17 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: T.257, A.258, R.279 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: S.145, K.146, E.147, N.177, A.178, D.179, Y.222 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: Q.3, V.9, N.235, P.236, I.237 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: Q.28, P.236, Q.238 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: P.12, Y.15, N.235 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain A: G.39, M.41 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain A: M.41, M.42, K.76 Ligands: EDO.27 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: M.20, L.21, L.22, Y.222, V.223, A.226 Ligand excluded by PLIP EDO.30: 8 residues within 4Å: Chain A: N.43, Y.47, G.71, A.72, G.73, G.81, D.130 Ligands: SAM.15 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: R.19, M.20, L.21, E.23 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain B: D.92, T.112, N.115 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 7 residues within 4Å: Chain B: C.75, H.84, F.90, C.91, D.92, L.93 Ligands: EDO.35 Ligand excluded by PLIP

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 Ligands: EDO.12 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.13, A:T.58

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

SAM.15: 20 residues within 4Å: Chain A: N.43, Y.47, 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, F.149 Ligands: ATP.1, EDO.30 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:G.71, 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, A:S.74, A:D.99 Salt bridges: A:D.130

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.32: 2 residues within 4Å: Chain A: D.220, M.224 Ligand excluded by PLIP CL.37: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.33: 4 residues within 4Å: Chain B: C.75, 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.34: 4 residues within 4Å: Chain B: C.118, 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

2023-05-31

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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