Research workbench
SARS-cov-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 global refinement
Analyse SARS-cov-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 global refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N8H
- Type
- protein
- Length
- 4,356 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2M11 Fab light chain variable region; S2M11 Fab heavy chain variable…
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K | Spike glycoprotein | protein | 999 | 23% helix, 35% strand | P0DTC2 |
| D, G, L | S2M11 Fab light chain variable region | protein | 104 | 3% helix, 55% strand | — |
| E, H, M | S2M11 Fab heavy chain variable region | protein | 122 | 12% helix, 48% strand | — |
| B, I, N | S2L20 Fab light chain variable region | protein | 106 | 3% helix, 48% strand | — |
| C, J, O | S2L20 Fab heavy chain variable region | protein | 121 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 57 copies · chains A, L, D, F, G, K, C, J, O
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains A, M, E, F, H, K
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 | 1176 | 0.87 | 0.88 | 130 | empty |
| 2 | 1193 | 0.85 | 0.86 | 142 | empty |
| 3 | 975 | 0.85 | 0.86 | 112 | empty |
| 4 | 1046 | 0.85 | 0.86 | 114 | empty |
| 5 | 1021 | 0.85 | 0.86 | 113 | empty |
Interfaces
30 interfaces between chains.
- A–F · 4585 Ų buried · 45 hydrogen bonds · protein-protein
- A–K · 4576 Ų buried · 45 hydrogen bonds · protein-protein
- F–K · 4574 Ų buried · 45 hydrogen bonds · protein-protein
- L–M · 810 Ų buried · 11 hydrogen bonds · protein-protein
- G–H · 804 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7N8H · SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 Global Refinement · 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 7N8H · PDBe 7N8H · UniProt P0DTC2
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