SMTL ID : 8otr.1

SARS-CoV-2 nsp10-16 methyltransferase in complex with SAM analog BDH 33959089

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150 Ligands: W08.28 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: H.119, A.121, V.289, I.290, S.291 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: K.24, N.138, V.139, K.141, N.143, E.173, H.174 Ligands: EDO.29 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: A.34, T.35, S.240, S.241, Y.242 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: D.179, K.182, H.186 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain A: T.117, L.295 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: R.66, N.122, K.123, E.284, N.285, N.286 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.2 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: K.16, M.17, W.190, E.217 Ligand excluded by PLIP EDO.14: 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.15: 3 residues within 4Å: Chain A: K.137, S.201, S.202 Ligand excluded by PLIP EDO.16: 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.17: 5 residues within 4Å: Chain A: N.55, T.56, L.57, T.58, R.255 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, A.105 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: Y.132, K.170, N.198, S.201, E.203 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: T.257, A.258, R.279 Ligand excluded by PLIP EDO.21: 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.22: 5 residues within 4Å: Chain A: Q.3, V.9, N.235, P.236, I.237 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: P.12, Y.15, N.235 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: G.39 Ligands: EDO.25 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain A: M.41, M.42, K.76 Ligands: EDO.24 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: M.20, L.21, L.22, V.223, A.226 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain A: R.19, M.20, L.21, E.23 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain A: L.22, E.23, K.24, E.142, N.143 Ligands: EDO.4 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain B: D.92, T.112, N.115, W.124 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain B: C.75, H.84, F.90, C.91, D.92, L.93 Ligand excluded by PLIP

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 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.13, A:T.58

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

SAM.13: 19 residues within 4Å: Chain A: N.43, Y.47, G.71, A.72, G.73, P.80, G.81, D.99, L.100, N.101, G.113, D.114, C.115, D.130, M.131, Y.132, F.149, K.170 Ligands: W08.28 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:G.71, A:G.73, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:N.101, A:N.101 Salt bridges: A:D.130

1 x W08: (2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-N-(1-methylpiperidin-4-yl)-3,4-bis(oxidanyl)oxolane-2-carboxamide(Non-covalent)

W08.28: 13 residues within 4Å: Chain A: D.99, L.100, D.114, C.115, A.116, M.131, Y.132, D.133, K.135, G.148, F.149 Ligands: EDO.1, SAM.13 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:D.99, A:D.99, A:L.100, A:C.115, A:D.133, A:K.135, A:F.149 Salt bridges: A:D.114 pi-Stacking: A:F.149

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

CL.30: 2 residues within 4Å: Chain A: D.220, M.224 Ligand excluded by PLIP

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

2023-05-24

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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