Research workbench
Structure of the SARS-cov-2 spike glycoprotein in complex with the 47D11 neutralizing antibody Fab fragment
Analyse Structure of the SARS-cov-2 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
- 7AKD
- Type
- protein
- Length
- 3,404 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 47D11 neutralizing antibody heavy chain; 47D11 neutralizing antibody…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 970 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 990 | 24% helix, 33% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 992 | 23% helix, 30% strand | P0DTC2 |
| D, H | 47D11 neutralizing antibody heavy chain | protein | 120 | 5% helix, 52% strand | — |
| E, L | 47D11 neutralizing antibody light chain | protein | 106 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, H, L, C, D, E
- MAN · alpha-D-mannopyranose · sugar · 8 copies · chains L, E, D, H
- BMA · beta-D-mannopyranose · sugar · 6 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains B, C, 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 | 830 | 0.86 | 0.88 | 95 | empty |
| 2 | 1098 | 0.86 | 0.87 | 112 | empty |
| 3 | 807 | 0.80 | 0.83 | 64 | empty |
| 4 | 1066 | 0.80 | 0.81 | 74 | empty |
| 5 | 177 | 0.75 | 0.91 | 29 | empty |
Interfaces
10 interfaces between chains.
- B–C · 4262 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3976 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 3507 Ų buried · 20 hydrogen bonds · protein-protein
- H–L · 833 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 822 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7AKD · Structure of the SARS-CoV-2 spike glycoprotein in complex with the 47D11 neutralizing… · 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 7AKD · PDBe 7AKD · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.