Nsp10-nsp16 complex

SAM-binding site

Cyanidin-3-O-glucoside

Code: 6YZ1_C3OG

Elenolic acid

Code: 6YZ1_ELA


Epigallocatechin gallate

Code: 6YZ1_EGCG


Details

Cyanidin-3-O-glucoside (Gromacs 2018.2, force field: CHARMM36):

6YZ1_C3OG-1: Cyanidin-3-O-glucoside bound to the SAM-binding site of nsp16 (200 ns, 109890 atoms)

6YZ1_C3OG-2: Cyanidin-3-O-glucoside bound to the SAM-binding site of nsp16 (200 ns, 109890 atoms)

6YZ1_C3OG-3: Cyanidin-3-O-glucoside bound to the SAM-binding site of nsp16 (200 ns, 109890 atoms)


Elenolic acid (Gromacs 2018.2, force field: CHARMM36): 

6YZ1_ELA-1: Elenolic acid bound to the SAM-binding site of nsp16 (100 ns, 109907 atoms)

6YZ1_ELA-2: Elenolic acid bound to the SAM-binding site of nsp16 (100 ns, 109907 atoms)

6YZ1_ELA-3: Elenolic acid bound to the SAM-binding site of nsp16 (100 ns, 109907 atoms)


Epigallocatechin gallate (Gromacs 2018.2, force field: CHARMM36):

6YZ1_EGCG-1: Epigallocatechin gallate bound to the SAM-binding site of nsp16 (200 ns, 109905 atoms)

6YZ1_EGCG-2: Epigallocatechin gallate bound to the SAM-binding site of nsp16 (200 ns, 109905 atoms)

6YZ1_EGCG-3: Epigallocatechin gallate bound to the SAM-binding site of nsp16 (200 ns, 109905 atoms)

Homovanillic acid

Code: 6YZ1_HVA

Hydroxytyrosol

Code: 6YZ1_HT


Ligstroside

Code: 6YZ1_US_LIGS

Details

Homovanillic acid (Gromacs 2018.2, force field: CHARMM36):

6YZ1_HVA-1: Homovanillic acid bound to the SAM-binding site of nsp16 (100 ns, 109914 atoms)

6YZ1_HVA-2: Homovanillic acid bound to the SAM-binding site of nsp16 (100 ns, 109914 atoms)

6YZ1_HVA-3: Homovanillic acid bound to the SAM-binding site of nsp16 (100 ns, 109914 atoms)


Hydroxytyrosol (Gromacs 2018.2, force field: CHARMM36): 

6YZ1_HT-1: Hydroxytyrosol bound to the SAM-binding site of nsp16 (100 ns, 109911 atoms)

6YZ1_HT-2: Hydroxytyrosol bound to the SAM-binding site of nsp16 (100 ns, 109911 atoms)

6YZ1_HT-3: Hydroxytyrosol bound to the SAM-binding site of nsp16 (100 ns, 109911 atoms)


Ligstroside (Gromacs 2020.4, force field: CHARMM36): 

6YZ1_US_LIGS-1: Ligstroside bound to the SAM-binding site of nsp16 (1000 ns, 109914 atoms)

6YZ1_US_LIGS-2: Ligstroside bound to the SAM-binding site of nsp16 (1000 ns, 109914 atoms)

6YZ1_US_LIGS-3: Ligstroside bound to the SAM-binding site of nsp16 (1000 ns, 109914 atoms)

Oleacein

Code: 6YZ1_OLEA

Oleuropein

Code: 6YZ1_OLEU

Oleuropein aglycone

Code: 6YZ1_OLAG; 6YZ1_US_OLAG

Details

Oleacein (Gromacs 2018.2, force field: CHARMM36): 

6YZ1_OLEA-1: Oleacein bound to the SAM-binding site of nsp16 (200 ns, 109903 atoms)

6YZ1_OLEA-2: Oleacein bound to the SAM-binding site of nsp16 (200 ns, 109903 atoms)

6YZ1_OLEA-3: Oleacein bound to the SAM-binding site of nsp16 (200 ns, 109903 atoms)


Oleuropein (Gromacs 2018.2, force field: CHARMM36): 

6YZ1_OLEU-1: Oleuropein bound to the SAM-binding site of nsp16 (206 ns, 109915 atoms)

6YZ1_OLEU-2: Oleuropein bound to the SAM-binding site of nsp16 (212 ns, 109915 atoms)

6YZ1_OLEU-3: Oleuropein bound to the SAM-binding site of nsp16 (202 ns, 109915 atoms)

6YZ1_OLEU-4: Oleuropein bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)

6YZ1_OLEU-5: Oleuropein bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)

6YZ1_OLEU-6: Oleuropein bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)


Oleuropein aglycone:

(Gromacs 2018.2, force field: CHARMM36)

6YZ1_OLAG-1: Oleuropein aglycone bound to the SAM-binding site of nsp16 (100 ns, 109918 atoms)

6YZ1_OLAG-2: Oleuropein aglycone bound to the SAM-binding site of nsp16 (100 ns, 109918 atoms)

6YZ1_OLAG-3: Oleuropein aglycone bound to the SAM-binding site of nsp16 (100 ns, 109918 atoms)

(Gromacs 2020.4, force field: CHARMM36)

6YZ1_OLAG-m1: Oleuropein aglycone bound to the SAM-binding site of nsp16 (93 ns, 109918 atoms)

6YZ1_OLAG-m2: Oleuropein aglycone bound to the SAM-binding site of nsp16 (84 ns, 109918 atoms)

6YZ1_OLAG-m3: Oleuropein aglycone bound to the SAM-binding site of nsp16 (142 ns, 109918 atoms)

6YZ1_US_OLAG-m4: Oleuropein aglycone bound to the SAM-binding site of nsp16 (1000 ns, 109918 atoms)

Sinefungin

Code: 6YZ1_SFG; 6YZ1_US_SFG

Vazegepant

Code: 6YZ1_US_VZGP 

Verbascoside

Code: 6YZ1_US_VERB 


Details

Sinefungin: 

(Gromacs 2018.2, force field: CHARMM36)

6YZ1_SFG-1: Sinefungin bound to the SAM-binding site of nsp16 (200 ns, 109915 atoms)

6YZ1_SFG-2: Sinefungin bound to the SAM-binding site of nsp16 (200 ns, 109915 atoms)

6YZ1_SFG-3: Sinefungin bound to the SAM-binding site of nsp16 (200 ns, 109915 atoms)

6YZ1_SFG-4: Sinefungin bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)

6YZ1_SFG-5: Sinefungin bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)

6YZ1_SFG-6: Sinefungin bound to the SAM-binding site of nsp16 (100 ns, 109915 atoms)

(Gromacs 2020.4, force field: CHARMM36)

6YZ1_US_SFG-1: Sinefungin bound to the SAM-binding site of nsp16 (1000 ns, 109915 atoms)

6YZ1_US_SFG-2: Sinefungin bound to the SAM-binding site of nsp16 (1000 ns, 109915 atoms)

6YZ1_US_SFG-3: Sinefungin bound to the SAM-binding site of nsp16 (1000 ns, 109915 atoms)


Vazegepant (Gromacs 2020.4, force field: CHARMM36): 

6YZ1_US_VZGP-1: Vazegepant bound to the SAM-binding site of nsp16 (1000 ns, 109902 atoms)

6YZ1_US_VZGP-2: Vazegepant bound to the SAM-binding site of nsp16 (1000 ns, 109902 atoms)

6YZ1_US_VZGP-3: Vazegepant bound to the SAM-binding site of nsp16 (1000 ns, 109902 atoms)


Verbascoside (Gromacs 2020.4, force field: CHARMM36): 

6YZ1_US_VERB-1: Verbascoside bound to the SAM-binding site of nsp16 (1000 ns, 109889 atoms)

6YZ1_US_VERB-2: Verbascoside bound to the SAM-binding site of nsp16 (1000 ns, 109889 atoms)

6YZ1_US_VERB-3: Verbascoside bound to the SAM-binding site of nsp16 (1000 ns, 109889 atoms)