8P9Y: SARS-CoV-2 S protein S:D614G mutant in 3-down with binding site of an entry inhibitor

PDB ID: 8P9YDownload
MMDB ID: 236202
PDB Deposition Date: 2023/6/6
Updated in MMDB: 2024/10
Experimental Method:
electron microscopy
Resolution: 4.3  Å
Source Organism:
Similar Structures:
Biological Unit for 8P9Y: trimeric; determined by author
Molecular Components in 8P9Y
Label Count Molecule
Proteins (3 molecules)
3
Spike Protein S1,spike Glycoprotein
Molecule annotation
Chemicals and Non-standard biopolymers (48 molecules)
1
44
2-acetamido-2-deoxy-beta-D-glucopyranose2-acetamido-2-deoxy-beta-D-glucopyranose
2
3
SODIUM IONSODIUM ION
3
1
[(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[(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
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303