Research workbench
Structure of coronavirus spike from smuggled guangdong pangolin
Analyse Structure of coronavirus spike from smuggled guangdong pangolin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BBH
- Type
- protein
- Length
- 3,189 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Surface glycoprotein
- UniProt
- A0A6M3G9R1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 1 distinct chain · 21% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Surface glycoprotein | protein | 1063 | 21% helix, 31% strand | A0A6M3G9R1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 69 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 | 317 | 0.86 | 0.95 | 34 | empty |
| 2 | 1160 | 0.85 | 0.86 | 126 | empty |
| 3 | 287 | 0.85 | 0.95 | 32 | empty |
| 4 | 493 | 0.85 | 0.91 | 63 | empty |
| 5 | 298 | 0.83 | 0.93 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 6185 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 6180 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 6111 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7BBH · Structure of Coronavirus Spike from Smuggled Guangdong Pangolin · 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 A0A6M3G9R1
- Elsewhere: RCSB PDB 7BBH · PDBe 7BBH · UniProt A0A6M3G9R1
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