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
- 7E3K
- Type
- protein
- Length
- 4,278 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 13G9 heavy chain; 13G9 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 16% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 990 | 22% helix, 28% strand | P0DTC2 |
| D, F, H | 13G9 heavy chain | protein | 221 | 3% helix, 48% strand | — |
| E, G, L | 13G9 light chain | protein | 215 | 4% helix, 41% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains A, B, C
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 | 1035 | 0.88 | 0.89 | 107 | empty |
| 2 | 1069 | 0.87 | 0.88 | 131 | empty |
| 3 | 697 | 0.74 | 0.80 | 47 | empty |
| 4 | 401 | 0.73 | 0.83 | 35 | empty |
| 5 | 800 | 0.71 | 0.77 | 51 | empty |
Interfaces
13 interfaces between chains.
- B–C · 3916 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 3910 Ų buried · 40 hydrogen bonds · protein-protein
- A–B · 3805 Ų buried · 26 hydrogen bonds · protein-protein
- F–G · 1446 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 1446 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 disulfide, 21 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3K · 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 7E3K · PDBe 7E3K · UniProt P0DTC2
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