Research workbench
A proof of concept for neutralizing antibody-guided vaccine design against SARS-cov-2
Analyse A proof of concept for neutralizing antibody-guided vaccine design against… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D4G
- Type
- protein
- Length
- 502 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein S1; Light chain of FC05 Fab; Heavy chain of FC05 Fab
- UniProt
- P0DTC2
- Pockets
- 7 · best druggability 0.41
Structure
electron microscopy · 3 distinct chains · 2% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Spike glycoprotein S1 | protein | 273 | 0% helix, 44% strand | P0DTC2 |
| G | Light chain of FC05 Fab | protein | 109 | 7% helix, 44% strand | — |
| N | Heavy chain of FC05 Fab | protein | 120 | 3% helix, 33% strand | — |
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 71 | 0.41 | 0.80 | 16 | empty |
| 2 | 67 | 0.41 | 0.80 | 16 | empty |
| 3 | 94 | 0.39 | 0.76 | 12 | empty |
| 4 | 50 | 0.38 | 0.81 | 16 | empty |
| 5 | 82 | 0.37 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- G–N · 905 Ų buried · 7 hydrogen bonds · protein-protein
- B–N · 763 Ų buried · 6 hydrogen bonds · protein-protein
- B–G · 100 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7D4G · A proof of concept for neutralizing antibody-guided vaccine design against SARS-CoV-2 · the same entry in another collection · chain B against B, 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 7D4G · PDBe 7D4G · UniProt P0DTC2
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