Research workbench
SARS-cov-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 (local refinement of the NTD/S2L20)
Analyse SARS-cov-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 (local refinement of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N8I
- Type
- protein
- Length
- 445 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2L20 Fab light chain variable region; S2L20 Fab heavy chain variable region; Spike…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 4 · best druggability 0.45
Structure
electron microscopy · 3 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | S2L20 Fab light chain variable region | protein | 106 | 3% helix, 48% strand | — |
| H | S2L20 Fab heavy chain variable region | protein | 121 | 5% helix, 50% strand | — |
| A | Spike glycoprotein | protein | 218 | 4% helix, 55% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.45 | 0.79 | 20 | empty |
| 2 | 129 | 0.41 | 0.75 | 25 | empty |
| 3 | 136 | 0.39 | 0.74 | 24 | empty |
| 4 | 87 | 0.35 | 0.75 | 20 | empty |
Interfaces
3 interfaces between chains.
- L–H · 913 Ų buried · 12 hydrogen bonds · protein-protein
- H–A · 716 Ų buried · 7 hydrogen bonds · protein-protein
- L–A · 202 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 7N8I · SARS-CoV-2 S (B.1.429 / epsilon variant) + S2M11 + S2L20 (Local Refinement of the… · 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 7N8I · PDBe 7N8I · UniProt P0DTC2
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