Research workbench
Structure of the SARS-cov-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment
Analyse Structure of the SARS-cov-2 spike glycoprotein in complex with the S309… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WPS
- Type
- protein
- Length
- 3,540 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S309 neutralizing antibody heavy chain; S309 neutralizing antibody…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 955 | 22% helix, 35% strand | P0DTC2 |
| H, C, F | S309 neutralizing antibody heavy chain | protein | 123 | 7% helix, 48% strand | — |
| L, D, G | S309 neutralizing antibody light chain | protein | 102 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, H, L, B, C, D, E, F, G
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains L, D, G
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains H, L, C, D, F, G
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 | 1103 | 0.86 | 0.87 | 141 | empty |
| 2 | 707 | 0.84 | 0.88 | 81 | empty |
| 3 | 750 | 0.79 | 0.83 | 84 | empty |
| 4 | 410 | 0.79 | 0.87 | 46 | empty |
| 5 | 506 | 0.77 | 0.85 | 57 | empty |
Interfaces
12 interfaces between chains.
- A–E · 4845 Ų buried · 43 hydrogen bonds · protein-protein
- B–E · 4837 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4833 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 737 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 736 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WPS · Structure of the SARS-CoV-2 spike glycoprotein in complex with the S309 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 6WPS · PDBe 6WPS · UniProt P0DTC2
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