SARS-CoV-2 S-protein:D614G mutant in 1-up conformation
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8p99
Q-score: 0.343
Gargantilla M, Frances C, Adhav A, Forcada-Nadal A, Martinez-Gualda B, Marti-Mari O, Lopez-Redondo ML, Melero R, Marco-Marin C, Gougeard N, Espinosa C, Rubio-Del-Campo A, Ruiz-Partida R, Hernandez-Sierra MDP, Villamayor-Belinchon L, Bravo J, Llacer JL, Marina A, Rubio V, San-Felix A, Geller R, Perez-Perez MJ
J Med Chem (2023) 66 pp. 10432-10457 [ Pubmed: 37471688 DOI: doi:10.1021/acs.jmedchem.3c00576 ]
SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor
Resolution: 4.3 Å
EM Method: Single-particle
Fitted PDBs: 8p9y
Q-score: 0.117
Gargantilla M, Frances C, Adhav A, Forcada-Nadal A, Martinez-Gualda B, Marti-Mari O, Lopez-Redondo ML, Melero R, Marco-Marin C, Gougeard N, Espinosa C, Rubio-Del-Campo A, Ruiz-Partida R, Hernandez-Sierra MDP, Villamayor-Belinchon L, Bravo J, Llacer JL, Marina A, Rubio V, San-Felix A, Geller R, Perez-Perez MJ
J Med Chem (2023) 66 pp. 10432-10457 [ Pubmed: 37471688 DOI: doi:10.1021/acs.jmedchem.3c00576 ]
- Sodium ion (22 Da, Ligand)
- [(2~{s})-2-[[4-(2-azanylethanoylamino)-7-[[(2~{s})-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-4-[3-[[(2~{s})-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]-1-oxidanylidene-1-sodiooxy-propan-2-yl]amino]-3-oxidanylidene-propyl]-7-oxidanylidene-heptanoyl]amino]-3-[2-(4-nitrophenyl)sulfanyl-1~{h}-indol-3-yl]propanoyl]oxysodium (1 kDa, Ligand)
- Spike protein s1,spike glycoprotein (140 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein - severe acute respiratory syndrome coronavirus 2 (Complex from Severe acute respiratory syndrome coronavirus 2)
Structure of the EVA71 strain 11316 capsid
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 6uh1
Q-score: 0.469
Martinez-Gualda B, Sun L, Marti-Mari O, Noppen S, Abdelnabi R, Bator CM, Quesada E, Delang L, Mirabelli C, Lee H, Schols D, Neyts J, Hafenstein S, Camarasa MJ, Gago F, San-Felix A
J Med Chem (2020) 63 pp. 349-368 [ Pubmed: 31809045 DOI: doi:10.1021/acs.jmedchem.9b01737 ]
- Sphingosine (299 Da, Ligand)
- Vp4 (7 kDa, Protein from Enterovirus A71)
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp2 (27 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
EV-A71 strain 11316 complexed with MADAL compound 22
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 6uh6
Q-score: 0.441
Martinez-Gualda B, Sun L, Marti-Mari O, Noppen S, Abdelnabi R, Bator CM, Quesada E, Delang L, Mirabelli C, Lee H, Schols D, Neyts J, Hafenstein S, Camarasa MJ, Gago F, San-Felix A
J Med Chem (2020) 63 pp. 349-368 [ DOI: doi:10.1021/acs.jmedchem.9b01737 Pubmed: 31809045 ]
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Vp4 (7 kDa, Protein from Enterovirus A71)
- Sphingosine (299 Da, Ligand)
- Enterovirus a71 (Virus from Enterovirus A71)
- Vp2 (26 kDa, Protein from Enterovirus A71)
EV-A71 strain 11316 complexed with MADAL compound 30
Resolution: 2.87 Å
EM Method: Single-particle
Fitted PDBs: 6uh7
Q-score: 0.468
Martinez-Gualda B, Sun L, Marti-Mari O, Noppen S, Abdelnabi R, Bator CM, Quesada E, Delang L, Mirabelli C, Lee H, Schols D, Neyts J, Hafenstein S, Camarasa MJ, Gago F, San-Felix A
J Med Chem (2020) 63 pp. 349-368 [ Pubmed: 31809045 DOI: doi:10.1021/acs.jmedchem.9b01737 ]
- Sphingosine (299 Da, Ligand)
- Vp4 (7 kDa, Protein from Enterovirus A71)
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp2 (27 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
Structure of the EVA71 strain 11316 capsid
Sun L, Lee H, Thibaut HJ, Lanko K, Rivero-Buceta E, Bator C, Martinez-Gualda B, Dallmeier K, Delang L, Leyssen P, Gago F, San-Felix A, Hafenstein S, Mirabelli C, Neyts J
PLoS Pathog (2019) 15 pp. e1007760-e1007760 [ DOI: doi:10.1371/journal.ppat.1007760 Pubmed: 31071193 ]
- Sphingosine (299 Da, Ligand)
- Vp2 (26 kDa, Protein from Enterovirus A71)
- Vp4 (7 kDa, Protein from Enterovirus A71)
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385
Resolution: 3.59 Å
EM Method: Single-particle
Fitted PDBs: 6diz
Q-score: 0.509
Sun L, Lee H, Thibaut HJ, Lanko K, Rivero-Buceta E, Bator C, Martinez-Gualda B, Dallmeier K, Delang L, Leyssen P, Gago F, San-Felix A, Hafenstein S, Mirabelli C, Neyts J
PLoS Pathog (2019) 15 pp. e1007760-e1007760 [ DOI: doi:10.1371/journal.ppat.1007760 Pubmed: 31071193 ]
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Sphingosine (299 Da, Ligand)
- Vp4 (8 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
- Vp2 (26 kDa, Protein from Enterovirus A71)