Research workbench
Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 43
Analyse Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 43 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L56
- Type
- protein
- Length
- 3,686 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 2-43 variable domain heavy chain; Fab 2-43 variable domain light…
- UniProt
- P0DTC2
- Ligands
- NAG, MAN, BMA, GAL
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 983 | 22% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 992 | 23% helix, 31% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 994 | 23% helix, 30% strand | P0DTC2 |
| F, H, J | Fab 2-43 variable domain heavy chain | protein | 129 | 7% helix, 43% strand | — |
| G, K, L | Fab 2-43 variable domain light chain | protein | 110 | 5% helix, 26% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains A, J, B, F, G, C, H
- MAN · alpha-D-mannopyranose · sugar · 9 copies · chains J, F, G, H, L
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains J, F, H
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains B, J, K, C, F, G, A, H, 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 | 724 | 0.82 | 0.86 | 96 | empty |
| 2 | 629 | 0.81 | 0.86 | 68 | empty |
| 3 | 1055 | 0.79 | 0.81 | 118 | empty |
| 4 | 671 | 0.79 | 0.84 | 73 | empty |
| 5 | 723 | 0.78 | 0.83 | 72 | empty |
Interfaces
15 interfaces between chains.
- A–B · 3963 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3873 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 3705 Ų buried · 27 hydrogen bonds · protein-protein
- H–L · 872 Ų buried · 6 hydrogen bonds · protein-protein
- J–K · 839 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7L56 · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-43 · 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 7L56 · PDBe 7L56 · UniProt P0DTC2
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