Research workbench
Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 4
Analyse Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XEY
- Type
- protein
- Length
- 3,788 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 2-4 heavy chain; 2-4 light chain
- UniProt
- P0DTC2, A0A5C2GJG2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1034 | 22% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1034 | 21% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1030 | 21% helix, 30% strand | P0DTC2 |
| F, H, J | 2-4 heavy chain | protein | 122 | 2% helix, 45% strand | — |
| G, K, L | 2-4 light chain | protein | 108 | 3% helix, 37% strand | A0A5C2GJG2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 58 copies · chains A, B, C, F, G, H, L, J, K
- BMA · beta-D-mannopyranose · sugar · 5 copies · chains J, K, A, H, L, B, 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 | 1050 | 0.83 | 0.84 | 100 | empty |
| 2 | 1188 | 0.81 | 0.82 | 138 | empty |
| 3 | 150 | 0.80 | 0.96 | 29 | empty |
| 4 | 799 | 0.78 | 0.82 | 67 | empty |
| 5 | 609 | 0.77 | 0.83 | 46 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4328 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 4320 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 4212 Ų buried · 32 hydrogen bonds · protein-protein
- J–K · 833 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 832 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 6XEY · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-4 · 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
- Every structure of UniProt A0A5C2GJG2
- Elsewhere: RCSB PDB 6XEY · PDBe 6XEY · UniProt P0DTC2 · UniProt A0A5C2GJG2
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