SMTL ID : 9guy.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and theophylline derivative LAS 54571098

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-mer

Ligands

23 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, S.175 Ligand excluded by PLIP EDO.3: 7 residues within 4Å: Chain A: H.119, T.120, A.121, V.289, I.290, S.291 Ligands: EDO.25 Ligand excluded by PLIP EDO.4: 10 residues within 4Å: Chain A: K.24, C.25, N.138, V.139, T.140, K.141, E.142, N.143, E.173, H.174 Ligand excluded by PLIP EDO.5: 6 residues within 4Å: Chain A: A.34, T.35, L.239, 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: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: T.117, D.293, V.294, L.295 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.25 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: A.10, Y.53, T.56, L.57, W.189 Ligands: MES.2 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain A: K.16, M.17, W.190, R.216, E.217, I.219, M.224 Ligand excluded by PLIP EDO.12: 11 residues within 4Å: Chain A: V.61, 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.13: 12 residues within 4Å: Chain A: L.27, Y.30, Y.132, K.137, T.172, E.173, S.200, S.201, S.202, E.203 Ligands: EDO.16, 01.19 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: N.55, T.56, L.57, T.58, R.255 Ligands: MES.2 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligands: EDO.31 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain A: K.46, Y.132, K.170, T.172, N.198, S.201, E.203 Ligands: EDO.13, SAM.20 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: Q.3, P.12, Y.15, W.231, N.235 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain A: G.39, I.40, M.41, M.42, K.76 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain A: M.20, L.21, E.23 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: W.5, Q.6, P.7, Q.52, S.243, D.246 Ligand excluded by PLIP EDO.25: 9 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligands: EDO.3, EDO.9 Ligand excluded by PLIP EDO.26: 9 residues within 4Å: Chain A: G.73, S.74, D.75, D.99, L.100, N.101, D.102, F.103 Ligands: SAM.20 Ligand excluded by PLIP EDO.29: 8 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, N.115, T.116, V.117, W.124 Ligand excluded by PLIP EDO.31: 9 residues within 4Å: Chain B: I.39, T.40, N.41, C.42, F.69, A.105, N.106, P.108 Ligands: EDO.15 Ligand excluded by PLIP

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

MES.2: 8 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 Ligands: EDO.10, EDO.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x 01: ~{N}-[(5~{S})-5-azanyl-6-[(3~{S},4~{S},6~{R})-3-[1,3-dimethyl-2,6-bis(oxidanylidene)purin-7-yl]-4-methyl-4,6-bis(oxidanyl)azepan-1-yl]-6-oxidanylidene-hexyl]ethanamide

01.19: 11 residues within 4Å: Chain A: K.24, C.25, D.26, L.27, Q.28, Y.30, G.31, K.137, V.139, S.202 Ligands: EDO.13 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.30 Hydrogen bonds: A:K.24, A:L.27, A:L.27 pi-Stacking: A:Y.30, A:Y.30 pi-Cation interactions: A:K.24

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

SAM.20: 23 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.16, EDO.26 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.47, A:A.72, A:G.81, A:D.99, A:D.99, A:L.100, A:C.115, A:D.130, A:Y.132 Water bridges: A:D.114, A:G.148, A:F.149 Salt bridges: A:D.130

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

CL.21: 4 residues within 4Å: Chain A: I.219, D.220, V.223, M.224 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain A: L.262, I.282 Ligand excluded by PLIP CL.30: 2 residues within 4Å: Chain B: I.39, R.79 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.27: 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.28: 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 SARS-CoV-2 methyltransferase nsp10-16 with Cap0-site binders. To Be Published

Release Date

2024-12-04

Peptides

2'-O-methyltransferase nsp16: A
Non-structural protein 10: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

2'-O-methyltransferase nsp16

Non-structural protein 10

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