MolNFT v1 · #190241 · protein
Cryo-EM structure of SARS-cov-2 C.1.2 S6P trimer in complex with neutralizing antibody vacw-209 (local refinement)
7WP2 · Vacw-209 light chain: “Cryo-EM structure of SARS-cov-2 C.1.2 S6P trimer in complex with neutralizing antibody vacw-209 (local…”. Electron microscopy, 1 ligand (NAG), 5 pockets (best druggability 0.45). MolNFT v1 #190241 on…
- PDB
- 7WP2
- Type
- protein
- Length
- 422 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vacw-209 light chain; Vacw-209 heavy chain; Spike protein S1
- UniProt
- A0A5C2GQT9, P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.45
Structure
electron microscopy · 3 distinct chains · 2% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Vacw-209 light chain | protein | 109 | 0% helix, 41% strand | A0A5C2GQT9 |
| H | Vacw-209 heavy chain | protein | 131 | 2% helix, 40% strand | — |
| F | Spike protein S1 | protein | 182 | 3% helix, 23% 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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.45 | 0.75 | 28 | empty |
| 2 | 157 | 0.43 | 0.75 | 28 | empty |
| 3 | 91 | 0.39 | 0.77 | 16 | empty |
| 4 | 76 | 0.34 | 0.75 | 16 | empty |
| 5 | 57 | 0.30 | 0.75 | 13 | empty |
Interfaces
3 interfaces between chains.
- L–H · 887 Ų buried · 7 hydrogen bonds · protein-protein
- H–F · 674 Ų buried · 1 hydrogen bond · protein-protein
- L–F · 417 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WP2 · Cryo-EM structure of SARS-CoV-2 C.1.2 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 7WP2 · PDBe 7WP2 · UniProt A0A5C2GQT9 · UniProt P0DTC2
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