Research workbench
Structure of formaldehyde cross-linked SARS-cov-2 S glycoprotein
Analyse Structure of formaldehyde cross-linked SARS-cov-2 S glycoprotein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q1Z
- Type
- protein
- Length
- 2,916 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 1 distinct chain · 23% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 972 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, C, B
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 | 1166 | 0.87 | 0.88 | 131 | empty |
| 2 | 813 | 0.86 | 0.88 | 99 | empty |
| 3 | 351 | 0.81 | 0.90 | 38 | empty |
| 4 | 454 | 0.80 | 0.88 | 60 | empty |
| 5 | 470 | 0.79 | 0.87 | 56 | empty |
Interfaces
3 interfaces between chains.
- B–C · 5324 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 5248 Ų buried · 42 hydrogen bonds · protein-protein
- A–C · 5231 Ų buried · 40 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 35 glycan (disulfide, N-glycosylation, glycation).
Compared structures
- 7Q1Z · Structure of formaldehyde cross-linked SARS-CoV-2 S glycoprotein · 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 7Q1Z · PDBe 7Q1Z · UniProt P0DTC2
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