Research workbench
Ultrapotent SARS-cov-2 neutralizing antibodies with protective efficacy against newly emerged mutational variants
Analyse Ultrapotent SARS-cov-2 neutralizing antibodies with protective efficacy against… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WS4
- Type
- protein
- Length
- 3,327 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 510A5 light chain; 510A5 heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1032 | 22% helix, 34% strand | P0DTC2 |
| H | 510A5 light chain | protein | 108 | 0% helix, 40% strand | — |
| I | 510A5 heavy chain | protein | 123 | 5% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 38 copies · chains C, B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 780 | 0.84 | 0.87 | 93 | empty |
| 2 | 555 | 0.82 | 0.87 | 35 | empty |
| 3 | 445 | 0.80 | 0.88 | 59 | empty |
| 4 | 819 | 0.80 | 0.83 | 87 | empty |
| 5 | 1014 | 0.79 | 0.81 | 93 | empty |
Interfaces
7 interfaces between chains.
- B–C · 5392 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4745 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4451 Ų buried · 35 hydrogen bonds · protein-protein
- H–I · 945 Ų buried · 6 hydrogen bonds · protein-protein
- C–I · 547 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 25 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7WS4 · Ultrapotent SARS-CoV-2 neutralizing antibodies with protective efficacy against newly… · the same entry in another collection · chain A against A, 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 P0DTC2
- Elsewhere: RCSB PDB 7WS4 · PDBe 7WS4 · UniProt P0DTC2
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