Export Alignment
Secondary Structure
None DSSP PSIPRED SSpro
Colour Scheme
Fade Mismatches Enhance Mismatches
Confidencegradient Confidenceclass Indels Chain Unique Chain Rainbow 2° Structure Clustal Hydrophobic Size Charged Polar Proline Ser/Thr Cysteine Aliphatic Aromatic No Colour
Use QMEANBrane values

Background |  |  |

3D Viewer
NGL PV

### 2'-O-methyltransferase nsp16 | P0DTD1 PRO_0000449633

### Created: May 5, 2023, 9:33 p.m. at 21:33

Order by:

Oligo-State
  Monomer
GMQE
  0.94
QMEANDisCo Global:
  0.88 ± 0.05

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-ADENOSYLMETHIONINE

  SAM.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).

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
--- | --- | ---
M7G-A-U-U-A | ✓ | RNA (5'-D(*(M7G))-R(P*AP*UP*UP*A)-3')
SAM | ✓ | S-ADENOSYLMETHIONINE
CL | ✕ - Not biologically relevant. | CHLORIDE ION
FMT | ✕ - Not biologically relevant. | FORMIC ACID
FMT | ✕ - Not biologically relevant. | FORMIC ACID
FMT | ✕ - Not biologically relevant. | FORMIC ACID
FMT | ✕ - Not biologically relevant. | FORMIC ACID
MG | ✕ - Not in contact with model. | MAGNESIUM ION
NA | ✕ - Not biologically relevant. | SODIUM ION
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION

Model-Template Alignment

Oligo-State
  Monomer
GMQE
  0.93
QMEANDisCo Global:
  0.86 ± 0.05

Ligands
  1 x SAM
  1 x S-ADENOSYLMETHIONINE

  SAM.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

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

Ligand | Added to Model | Description
--- | --- | ---
SAM | ✓ | S-ADENOSYLMETHIONINE
ZN | ✕ - Binding site not conserved. | ZINC ION
ZN | ✕ - Binding site not conserved. | ZINC ION

Model-Template Alignment

Click model image to view in 3D
Click model image to view in 3D

### Delete Model - ""

Are you sure you want to delete this model?
(This really can't be undone!)