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2'-O-methyltransferase nsp16 | P0DTD1 PRO_0000449633
Created: May 5, 2023 at 21:33
Model 01
- Ligands
1 x M7G-A-U-U-A ,1 x SAM 1 x RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')M7G-A-U-U-A.1: 30 residues within 4Å:- Chain A: K.24, C.25, D.26, L.27, Y.30, S.33, A.34, L.36, M.42, N.43, K.46, S.74, D.75, K.76, Y.132, P.134, K.137, K.170, T.172, E.173, H.174, S.175, N.198, S.201, S.202, E.203,
- Ligand: M7G,A,U,U,A.1, M7G,A,U,U,A.1, M7G,A,U,U,A.1, M7G,A,U,U,A.1
18 PLIP interactions:18 interactions with chain A- Hydrogen bonds: A:K.24, A:L.27, A:Y.30, A:Y.132, A:K.137, A:T.172, A:T.172, A:H.174, A:S.175, A:S.202, A:S.202
- Salt bridges: A:K.137, A:K.137, A:H.174
- pi-Stacking: A:Y.30, A:Y.30
- pi-Cation interactions: A:K.24, A:Y.30
1 x S-ADENOSYLMETHIONINESAM.2: 20 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,
- Ligand: M7G,A,U,U,A.1, M7G,A,U,U,A.1
11 PLIP interactions:11 interactions with chain A- Hydrogen bonds: A:N.43, A:G.71, A:G.73, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132
- Salt bridges: A:D.130
QMEANDisCo Local
QMEAN Z-Scores
Template
7jyy.1.A
2'-O-methyltransferase
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).
Crystal Structure of SARS-CoV-2 Nsp16/10 Heterodimer in Complex with (m7GpppA)pUpUpApApA (Cap-0) and S-Adenosylmethionine (SAM).
- Seq Identity
- 100.00%
- Coverage
| Biounit Oligo State | Hetero-dimer |
| QSQE | 0.00 |
| Method | X-ray, 2.05 Å |
| Seq Similarity | 0.62 |
| Coverage | 1.00 |
| Range | 1-298 |
| Ligand | Added to Model | Description |
|---|---|---|
| ✓ | RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3') | |
| ✓ | S-ADENOSYLMETHIONINE | |
| ✕ - Not biologically relevant. | CHLORIDE ION | |
| ✕ - Not biologically relevant. | FORMIC ACID | |
| ✕ - Not biologically relevant. | FORMIC ACID | |
| ✕ - Not biologically relevant. | FORMIC ACID | |
| ✕ - Not biologically relevant. | FORMIC ACID | |
| ✕ - Not in contact with model. | MAGNESIUM ION | |
| ✕ - Not biologically relevant. | SODIUM ION | |
| ✕ - Binding site not conserved. | ZINC ION | |
| ✕ - Binding site not conserved. | ZINC ION |
Model-Template Alignment
Model 02
- Ligands
1 x SAM 1 x S-ADENOSYLMETHIONINESAM.1: 18 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
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:N.43, A:G.71, A:G.73, A:G.81, A:L.100, A:N.101, A:D.114, A:C.115, A:Y.132
- Salt bridges: A:D.130
QMEANDisCo Local
QMEAN Z-Scores
Template
7bq7.1.A
2'-O-methyltransferase
Crystal structure of 2019-nCoV nsp16-nsp10 complex
Crystal structure of 2019-nCoV nsp16-nsp10 complex
- Seq Identity
- 100.00%
- Coverage
| Biounit Oligo State | Hetero-dimer |
| QSQE | 0.00 |
| Method | X-ray, 2.37 Å |
| Seq Similarity | 0.62 |
| Coverage | 1.00 |
| Range | 1-297 |
Model-Template Alignment
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