SMTL ID : 8ov1.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

hetero-1-1-mer

Ligands

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

EDO.1: 9 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 Ligands: EDO.20 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: H.119, T.120, 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, E.142, N.143, E.173, H.174 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: S.33, A.34, T.35, L.239, S.240, S.241, Y.242 Ligands: EDO.14 Ligand excluded by PLIP EDO.6: 9 residues within 4Å: Chain A: L.27, Y.30, Y.132, K.137, T.172, S.200, S.201, S.202, E.203 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: T.35, L.36, P.37, K.38 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain A: T.117, D.293, V.294, L.295 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: M.20, L.21, E.23, F.230 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: K.16, M.17, W.190, E.217, Q.218, I.219, M.224 Ligands: EDO.30 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: M.20, L.21, L.22, Y.222, V.223, A.226 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: V.259, M.260, S.261, R.283, E.284, N.285 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain A: D.32, S.33, A.34, L.239 Ligands: EDO.5 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.100, N.101, D.102, I.112 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: R.255, G.256, T.257, A.258, G.278, R.279 Ligand excluded by PLIP EDO.17: 13 residues within 4Å: Chain A: N.43, Y.47, H.69, G.71, A.72, G.73, S.74, A.79, P.80, G.81, T.82, D.130 Ligands: SAM.29 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: D.102, F.103, V.104, S.105, T.110, I.112 Chain B: K.94 Ligands: EDO.22 Ligand excluded by PLIP EDO.20: 6 residues within 4Å: Chain A: T.136, S.145, K.146, E.147, G.148 Ligands: EDO.1 Ligand excluded by PLIP EDO.21: 9 residues within 4Å: Chain A: P.62, Y.63, N.64, M.65, P.90, T.91, G.92, T.93, L.254 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: T.110, L.111, I.112, S.292, V.294 Ligands: EDO.19 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain A: Q.3, P.12, Y.15, W.231, N.235 Ligand excluded by PLIP EDO.24: 9 residues within 4Å: Chain A: L.54, N.55, T.56, L.57, T.58, L.59, V.61, L.252, R.255 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain A: W.5, Q.6, P.7, Q.52, S.243, D.246 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain A: K.123, L.163, L.262, K.263, E.264, I.267, I.282 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain A: R.19, Q.218, I.219, D.220 Ligands: EDO.30 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 Ligand excluded by PLIP EDO.30: 11 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.11, EDO.27 Ligand excluded by PLIP EDO.31: 6 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, F.69, A.105, N.106 Ligand excluded by PLIP EDO.34: 11 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 Ligands: EDO.35, EDO.36 Ligand excluded by PLIP EDO.35: 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.34, EDO.36 Ligand excluded by PLIP EDO.36: 10 residues within 4Å: Chain B: C.74, C.75, L.76, Y.77, L.93, V.109, T.112, L.113 Ligands: EDO.34, EDO.35 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, C.209 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.13, A:T.58, A:W.189

1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.18: 16 residues within 4Å: Chain A: G.71, G.73, S.74, 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.29 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.73, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132 Water bridges: A:G.71, A:D.99 Salt bridges: A:K.170

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

SAM.29: 21 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, K.170 Ligands: EDO.17, ADP.18 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:N.43, A:Y.47, A:G.71, A:G.73, A:G.81, A:L.100, 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

2 x ZN: ZINC ION(Non-covalent)

ZN.32: 5 residues within 4Å: Chain B: C.75, Y.77, 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.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., 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

2023-05-10

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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