Research workbench
Structure of the SARS-cov spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment
Analyse Structure of the SARS-cov spike glycoprotein in complex with the 47D11… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AKJ
- Type
- protein
- Length
- 3,930 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 47D11 neutralizing antibody heavy chain; 47D11 neutralizing antibody…
- UniProt
- Q5DIC5
- Ligands
- NAG, MAN, FUC, BMA
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, B, A | Spike glycoprotein | protein | 1084 | 22% helix, 32% strand | Q5DIC5 |
| G, E, H | 47D11 neutralizing antibody heavy chain | protein | 120 | 8% helix, 52% strand | — |
| F, D, L | 47D11 neutralizing antibody light chain | protein | 106 | 3% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains C, B, G, F, A, E, D, H, L
- MAN · alpha-D-mannopyranose · sugar · 15 copies · chains G, F, E, D, H, L
- FUC · alpha-L-fucopyranose · sugar · 6 copies · chains C, B, A
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 975 | 0.87 | 0.88 | 111 | empty |
| 2 | 1126 | 0.84 | 0.85 | 128 | empty |
| 3 | 949 | 0.79 | 0.81 | 102 | empty |
| 4 | 1200 | 0.79 | 0.80 | 103 | empty |
| 5 | 1069 | 0.79 | 0.80 | 117 | empty |
Interfaces
15 interfaces between chains.
- C–A · 4784 Ų buried · 26 hydrogen bonds · protein-protein
- C–B · 4783 Ų buried · 24 hydrogen bonds · protein-protein
- B–A · 4782 Ų buried · 25 hydrogen bonds · protein-protein
- G–F · 858 Ų buried · 3 hydrogen bonds · protein-protein
- E–D · 854 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 45 glycan (disulfide, N-glycosylation).
Compared structures
- 7AKJ · Structure of the SARS-CoV spike glycoprotein in complex with the 47D11 neutralizing… · the same entry in another collection · chain C against C, 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 Q5DIC5
- Elsewhere: RCSB PDB 7AKJ · PDBe 7AKJ · UniProt Q5DIC5
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