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
- 7E3L
- Type
- protein
- Length
- 4,266 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 58G6 heavy chain; 58G6 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 986 | 23% helix, 27% strand | P0DTC2 |
| H, F, D | 58G6 heavy chain | protein | 221 | 5% helix, 44% strand | — |
| L, G, E | 58G6 light chain | protein | 215 | 7% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 20 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 | 1087 | 0.87 | 0.88 | 132 | empty |
| 2 | 741 | 0.86 | 0.89 | 78 | empty |
| 3 | 685 | 0.73 | 0.80 | 39 | empty |
| 4 | 794 | 0.73 | 0.78 | 68 | empty |
| 5 | 691 | 0.72 | 0.78 | 48 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4055 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 4037 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 3974 Ų buried · 29 hydrogen bonds · protein-protein
- D–E · 1688 Ų buried · 3 hydrogen bonds · protein-protein
- F–G · 1679 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 20 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3L · 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 7E3L · PDBe 7E3L · UniProt P0DTC2
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