SMTL ID : 8c5m.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 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.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, I.290, S.291 Ligands: EDO.30 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Y.132, K.170, N.198, S.201, E.203 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: K.24, N.138, V.139, K.141, N.143, E.173, H.174 Ligands: EDO.7 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: L.22, E.23, E.142, N.143 Ligands: EDO.6 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: A.34, T.35, L.239, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.9: 3 residues within 4Å: Chain A: K.137, S.201, S.202 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: V.118, H.119, T.120, F.156, Q.159, K.160 Ligands: EDO.21 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: Q.158, D.179, K.182, H.186 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57 Ligands: MES.3 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: T.117, D.293, L.295 Ligands: EDO.29 Ligand excluded by PLIP EDO.17: 10 residues within 4Å: Chain A: K.16, M.17, Q.18, R.19, I.219, D.220, V.223, M.224, N.227 Ligands: EDO.23 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: M.20, L.21, L.22, Y.222, V.223, A.226 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: R.66, A.121, N.122, K.123, E.284, N.285, N.286, R.287 Ligand excluded by PLIP EDO.20: 12 residues within 4Å: Chain A: N.43, Y.47, H.69, G.71, A.72, G.73, S.74, P.80, G.81, D.130 Ligands: MTA.16, EDO.26 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.12, EDO.24 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: R.19, M.20, L.21, E.23 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, I.219, M.224 Ligands: EDO.17 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: A.116, G.148, T.151, Y.152 Ligands: EDO.21 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: S.273, S.276, K.277 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: M.41, N.43, S.74, D.75, K.76, V.78, P.80 Chain B: N.41 Ligands: EDO.20 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain A: Q.158, H.186, Y.211, G.213, K.214, P.215 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: L.163, L.212, G.213, K.214, E.264, I.267, L.272 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: A.116, T.117, H.119, D.293 Ligands: EDO.15 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain A: H.119, S.291 Ligands: EDO.4 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: D.92, T.112, N.115 Ligands: EDO.35, EDO.36 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: I.39, T.40, N.41, R.79 Ligands: EDO.37 Ligand excluded by PLIP EDO.35: 10 residues within 4Å: Chain B: C.74, C.75, L.76, Y.77, L.93, V.109, T.112, L.113 Ligands: EDO.33, EDO.36 Ligand excluded by PLIP EDO.36: 11 residues within 4Å: Chain B: C.75, Y.77, H.84, P.85, N.86, F.90, C.91, D.92, L.93 Ligands: EDO.33, EDO.35 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: I.39, R.79, C.80 Ligands: EDO.34 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.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x MTA: 5'-DEOXY-5'-METHYLTHIOADENOSINE(Non-covalent)

MTA.16: 13 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, F.149 Ligands: EDO.20 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.73, A:L.100, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:N.101

2 x ZN: ZINC ION(Non-covalent)

ZN.31: 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.32: 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

2023-03-01

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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