Research workbench
SARS-cov-2 S ntd B.1.1.529 omicron variant + S309 local refinement
Analyse SARS-cov-2 S ntd B.1.1.529 omicron variant + S309 local refinement in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7TLZ
- Type
- protein
- Length
- 475 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 0.66
Structure
electron microscopy · 3 distinct chains · 3% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S2L20 Fab light chain | protein | 104 | 0% helix, 45% strand | — |
| B | S2L20 Fab heavy chain | protein | 120 | 5% helix, 48% strand | — |
| J | Spike glycoprotein | protein | 251 | 3% helix, 54% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains J, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 499 | 0.66 | 0.77 | 58 | empty |
| 2 | 60 | 0.63 | 0.93 | 23 | empty |
| 3 | 105 | 0.51 | 0.82 | 20 | empty |
| 4 | 86 | 0.45 | 0.80 | 18 | empty |
| 5 | 101 | 0.37 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–B · 883 Ų buried · 8 hydrogen bonds · protein-protein
- B–J · 730 Ų buried · 4 hydrogen bonds · protein-protein
- A–J · 187 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 7TLZ · SARS-CoV-2 S NTD B.1.1.529 Omicron variant + S309 Local 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 7TLZ · PDBe 7TLZ · UniProt P0DTC2
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