Research workbench
Cryo-EM structure of SARS-cov-2 omicron S6P trimer in complex with neutralizing antibody vacw-209 (local refinement)
Analyse Cryo-EM structure of SARS-cov-2 omicron S6P trimer in complex with neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WP5
- Type
- protein
- Length
- 425 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacw-209 light chain; Vacw-209 heavy chain; Spikeprotein S1
- UniProt
- A0A5C2GQT9, P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.56
Structure
electron microscopy · 3 distinct chains · 1% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Vacw-209 light chain | protein | 111 | 0% helix, 33% strand | A0A5C2GQT9 |
| H | Vacw-209 heavy chain | protein | 131 | 0% helix, 47% strand | — |
| F | Spikeprotein S1 | protein | 183 | 3% helix, 14% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 77 | 0.56 | 0.86 | 28 | empty |
| 2 | 165 | 0.52 | 0.79 | 28 | empty |
| 3 | 226 | 0.49 | 0.75 | 35 | empty |
| 4 | 169 | 0.44 | 0.75 | 31 | empty |
| 5 | 91 | 0.38 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- L–H · 960 Ų buried · 7 hydrogen bonds · protein-protein
- H–F · 708 Ų buried · 6 hydrogen bonds · protein-protein
- L–F · 422 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WP5 · Cryo-EM structure of SARS-CoV-2 Omicron S6P trimer in complex with neutralizing antibody… · the same entry in another collection · chain L against L, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt A0A5C2GQT9
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7WP5 · PDBe 7WP5 · UniProt A0A5C2GQT9 · UniProt P0DTC2
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