SMTL ID : 8bsd.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93, L.94, L.254 Ligand excluded by PLIP EDO.2: 9 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 Ligands: TBN.20 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligands: EDO.9 Ligand excluded by PLIP EDO.5: 9 residues within 4Å: Chain A: K.24, C.25, N.138, V.139, K.141, E.142, N.143, E.173, H.174 Ligand excluded by PLIP EDO.6: 8 residues within 4Å: Chain A: S.33, A.34, T.35, L.239, S.240, S.241, Y.242 Ligands: EDO.17 Ligand excluded by PLIP EDO.7: 9 residues within 4Å: Chain A: L.27, Y.132, K.137, T.172, S.200, S.201, S.202, E.203 Ligands: EDO.22 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligands: EDO.4, EDO.13 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: T.117, D.293, V.294, L.295 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: L.100, N.101, D.102, I.112 Ligand excluded by PLIP EDO.13: 7 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.9, EDO.24 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: D.102, F.103, V.104, S.105, T.110, I.112 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain A: N.55, T.56, L.57, T.58, K.253, R.255 Ligands: MES.3 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.3 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: D.32, S.33, A.34, L.239 Ligands: EDO.6, EDO.18 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain A: Q.28, N.29, P.236, I.237, Q.238 Ligands: EDO.17 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: Q.3, P.12, Y.15, W.231, N.235 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain A: R.19, D.220, V.223 Ligand excluded by PLIP EDO.22: 8 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: EDO.7 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain A: R.255, G.256, T.257, A.258, G.278, R.279 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain A: A.116, H.119, T.151, Y.152 Ligands: EDO.13 Ligand excluded by PLIP EDO.25: 7 residues within 4Å: Chain A: W.5, Q.6, P.7, Q.52, S.243, D.246, K.249 Ligand excluded by PLIP EDO.26: 3 residues within 4Å: Chain A: S.273, S.276, K.277 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: E.23, F.230, N.233, T.234 Ligands: EDO.28 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain A: M.20, L.21, E.23, F.230 Ligands: EDO.27 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligands: EDO.37 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, N.115, T.116, V.117, W.124 Ligands: EDO.36 Ligand excluded by PLIP EDO.35: 2 residues within 4Å: Chain B: M.64, D.65 Ligand excluded by PLIP EDO.36: 10 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.34 Ligand excluded by PLIP EDO.37: 11 residues within 4Å: Chain A: M.41 Chain B: I.39, T.40, N.41, C.42, F.69, A.105, N.106, D.107, P.108 Ligands: EDO.31 Ligand excluded by PLIP

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

MES.3: 8 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 Ligands: EDO.15, EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x TBN: '2-(4-AMINO-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-3,4-DIOL(Non-covalent)

TBN.20: 14 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, D.133, F.149 Ligands: EDO.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.149 Hydrogen bonds: A:D.99, A:L.100, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:G.73, A:D.130

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

CL.29: 4 residues within 4Å: Chain A: I.219, D.220, V.223, M.224 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain A: L.22, E.142, N.143 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.32: 6 residues within 4Å: Chain B: C.75, Y.77, C.78, H.84, C.91, K.94 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.75, B:C.78, B:H.84, B:C.91 ZN.33: 6 residues within 4Å: Chain B: C.118, V.120, C.121, K.125, 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., Crystal structures of Tubercidin bound to the active site of the SARS-CoV-2 methyltransferase nsp10-16. To Be Published

Release Date

2022-12-07

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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