Research workbench
Structure of the SARS-cov-2 spike glycoprotein in complex with the S309 neutralizing antibody Fab fragment (open state)
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
- 6WPT
- Type
- protein
- Length
- 3,277 residues
- Chains
- 7
- 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, BMA, FUC, MAN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 6 distinct chains · 21% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 945 | 23% helix, 33% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 937 | 23% helix, 34% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 952 | 23% helix, 34% strand | P0DTC2 |
| H, D | S309 neutralizing antibody heavy chain | protein | 123 | 5% helix, 48% strand | — |
| L | S309 neutralizing antibody light chain | protein | 99 | 3% helix, 45% strand | — |
| E | S309 neutralizing antibody light chain | protein | 98 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 59 copies · chains A, D, E, B, C, L
- BMA · beta-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains D, E, H, L
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains L
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 | 1133 | 0.87 | 0.88 | 131 | empty |
| 2 | 947 | 0.86 | 0.87 | 122 | empty |
| 3 | 461 | 0.82 | 0.89 | 45 | empty |
| 4 | 827 | 0.81 | 0.84 | 82 | empty |
| 5 | 565 | 0.74 | 0.81 | 81 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4559 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4073 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 3720 Ų buried · 35 hydrogen bonds · protein-protein
- H–L · 757 Ų buried · 6 hydrogen bonds · protein-protein
- C–H · 712 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 47 glycan, 40 disulfide (N-glycosylation, disulfide).
Compared structures
- 6WPT · 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 6WPT · PDBe 6WPT · UniProt P0DTC2
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