SMTL ID : 9eml.1

SARS-CoV-2 methyltransferase nsp10-16 in complex with SAM and m7GpppA (Cap0-analog)/m7GpppAm (Cap1-analog)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-mer

Ligands

1 x GTA: P1-7-METHYLGUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE(Non-covalent)

GTA.1: 22 residues within 4Å: Chain A: C.25, D.26, L.27, Y.30, K.46, Y.132, P.134, T.136, K.137, V.139, K.170, T.172, E.173, H.174, S.175, N.198, S.201, S.202, E.203 Ligands: SAM.3, EDO.5, V9G.16 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:Y.30, A:K.46, A:Y.132, A:Y.132, A:K.137, A:K.170, A:T.172, A:H.174, A:H.174, A:S.175, A:N.198, A:S.201, A:S.202, A:S.202, A:E.203 Water bridges: A:N.43, A:N.198 Salt bridges: A:K.137, A:K.137, A:K.137 pi-Stacking: A:Y.30, A:Y.132

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

EDO.2: 8 residues within 4Å: Chain A: K.38, G.39 Chain B: K.44, E.67, F.69, A.105, N.106 Ligands: EDO.19 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.38, B:K.44 EDO.5: 7 residues within 4Å: Chain A: N.43, S.74, D.75, K.76 Ligands: GTA.1, SAM.3, V9G.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.75, A:D.75 EDO.6: 8 residues within 4Å: Chain A: V.118, H.119, T.120, Y.152, F.156, Q.159, K.160 Ligands: EDT.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.119, A:T.120, A:Q.159, A:K.160 EDO.7: 7 residues within 4Å: Chain A: L.163, L.262, K.263, E.264, I.267, I.282, R.283 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.123, A:L.262, A:L.262 EDO.8: 6 residues within 4Å: Chain A: A.121, N.122, K.123, Q.159, K.160, E.284 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.123, A:K.160 EDO.9: 7 residues within 4Å: Chain A: L.22, E.23, K.24, E.142, N.143, E.173, H.174 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.22 Water bridges: A:E.23, A:C.25, A:N.143 EDO.10: 3 residues within 4Å: Chain A: Q.18, R.19, M.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.18, A:R.19 Water bridges: A:Q.18 EDO.11: 8 residues within 4Å: Chain A: D.133, T.136, K.146, E.147, G.148, F.149, F.150, S.175 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.133, A:T.136, A:F.149 Water bridges: A:D.133, A:T.136 EDO.12: 6 residues within 4Å: Chain A: Q.28, N.29, P.236, I.237, Q.238, L.239 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.29, A:L.239 EDO.14: 7 residues within 4Å: Chain A: K.16, M.17, W.190, R.216, E.217, I.219, M.224 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.190, A:R.216, A:E.217 EDO.15: 6 residues within 4Å: Chain A: C.154, Q.158, D.179, K.182, L.183, H.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.179, A:H.186 EDO.19: 10 residues within 4Å: Chain B: I.39, T.40, N.41, C.42, K.44, F.69, A.105, N.106, P.108 Ligands: EDO.2 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:I.39, B:C.42, B:A.105 EDO.20: 9 residues within 4Å: Chain B: I.56, D.92, L.93, T.112, L.113, N.115, T.116, V.117, W.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.92

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

SAM.3: 25 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, P.134, F.149, K.170 Ligands: GTA.1, EDO.5, V9G.16 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:N.43, A:G.73, A:G.81, A:D.99, A:L.100, A:N.101, A:D.114, A:C.115, A:D.130, A:Y.132 Water bridges: A:G.71 Salt bridges: A:D.130

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

MES.4: 6 residues within 4Å: Chain A: N.13, T.56, L.57, T.58, W.189, C.209 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.58, A:W.189

1 x EDT: {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID(Non-covalent)

EDT.13: 9 residues within 4Å: Chain A: A.116, H.119, G.148, T.151, Y.152, G.155, F.156, Q.159 Ligands: EDO.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.155, A:Q.159 Water bridges: A:Q.158

1 x V9G: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-(2'-O-METHYL)-ADENOSINE(Non-covalent)

V9G.16: 23 residues within 4Å: Chain A: C.25, D.26, L.27, Y.30, N.43, K.46, Y.132, P.134, T.136, K.137, V.139, K.170, T.172, E.173, H.174, S.175, N.198, S.201, S.202, E.203 Ligands: GTA.1, SAM.3, EDO.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:L.27, A:Y.30, A:K.46, A:Y.132, A:K.137, A:K.170, A:T.172, A:T.172, A:H.174, A:H.174, A:S.175, A:N.198, A:S.201, A:S.201, A:S.202, A:S.202 Water bridges: A:N.43, A:N.198, A:S.201 Salt bridges: A:K.137, A:K.137, A:K.137 pi-Stacking: A:Y.30, A:Y.132

2 x ZN: ZINC ION(Non-covalent)

ZN.17: 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.18: 5 residues within 4Å: Chain B: C.118, V.120, 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

2024-03-20

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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