Research workbench
SARS-cov-2 S ntd B.1.617.1 kappa variant S2L20 local refinement
Analyse SARS-cov-2 S ntd B.1.617.1 kappa variant S2L20 local refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SOD
- Type
- protein
- Length
- 473 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S2L20 Fab light chain; S2L20 Fab heavy chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.56
Structure
electron microscopy · 3 distinct chains · 3% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | S2L20 Fab light chain | protein | 107 | 0% helix, 50% strand | — |
| H | S2L20 Fab heavy chain | protein | 121 | 5% helix, 49% strand | — |
| A | Spike glycoprotein | protein | 245 | 3% helix, 57% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.56 | 0.81 | 26 | empty |
| 2 | 249 | 0.53 | 0.76 | 36 | empty |
| 3 | 112 | 0.48 | 0.80 | 23 | empty |
| 4 | 81 | 0.36 | 0.76 | 24 | empty |
| 5 | 91 | 0.35 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 922 Ų buried · 9 hydrogen bonds · protein-protein
- H–A · 799 Ų buried · 6 hydrogen bonds · protein-protein
- L–A · 212 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7SOD · SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement · the same entry in another collection · chain L against L, 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 7SOD · PDBe 7SOD · UniProt P0DTC2
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