Research workbench
SARS-cov-2 S B.1.1.529 omicron variant + S309 + S2L20 global refinement
Analyse SARS-cov-2 S B.1.1.529 omicron variant + S309 + 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
- 7TM0
- Type
- protein
- Length
- 4,401 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2L20 Fab light chain; S2L20 Fab heavy chain; S309 Fab heavy chain…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 9 distinct chains · 19% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1016 | 22% helix, 36% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1015 | 22% helix, 36% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1012 | 23% helix, 35% strand | P0DTC2 |
| D, F, H | S2L20 Fab light chain | protein | 104 | 0% helix, 45% strand | — |
| E, G, I | S2L20 Fab heavy chain | protein | 120 | 5% helix, 48% strand | — |
| J | S309 Fab heavy chain | protein | 126 | 7% helix, 50% strand | — |
| K, M | S309 Fab light chain | protein | 101 | 3% helix, 47% strand | — |
| L, N | S309 Fab heavy chain | protein | 127 | 7% helix, 50% strand | — |
| O | S309 Fab light chain | protein | 104 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 52 copies · chains B, A, C
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 | 706 | 0.87 | 0.91 | 74 | empty |
| 2 | 1008 | 0.86 | 0.86 | 124 | empty |
| 3 | 1071 | 0.83 | 0.84 | 145 | empty |
| 4 | 1070 | 0.83 | 0.84 | 88 | empty |
| 5 | 907 | 0.81 | 0.83 | 109 | empty |
Interfaces
23 interfaces between chains.
- A–C · 4034 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 3729 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 3553 Ų buried · 32 hydrogen bonds · protein-protein
- A–I · 548 Ų buried · 4 hydrogen bonds · protein-protein
- B–G · 392 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 54 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 7TM0 · SARS-CoV-2 S B.1.1.529 Omicron variant + S309 + 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 7TM0 · PDBe 7TM0 · UniProt P0DTC2
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