Research workbench
Crystal structure of the SARS-cov spike protein fusion core
Analyse Crystal structure of the SARS-cov spike protein fusion core in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WNC
- Type
- protein
- Length
- 454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E2 glycoprotein
- UniProt
- P59594
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 6 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E2 glycoprotein | protein | 69 | 78% helix, 0% strand | P59594 |
| B | E2 glycoprotein | protein | 81 | 72% helix, 0% strand | P59594 |
| C | E2 glycoprotein | protein | 78 | 72% helix, 0% strand | P59594 |
| D | E2 glycoprotein | protein | 77 | 70% helix, 0% strand | P59594 |
| E | E2 glycoprotein | protein | 74 | 62% helix, 0% strand | P59594 |
| F | E2 glycoprotein | protein | 75 | 60% helix, 0% strand | P59594 |
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 58 | 0.72 | 0.97 | 16 | empty |
| 2 | 50 | 0.70 | 0.98 | 14 | empty |
| 3 | 54 | 0.69 | 0.97 | 18 | empty |
| 4 | 130 | 0.68 | 0.89 | 16 | empty |
| 5 | 334 | 0.65 | 0.80 | 45 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1182 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 1147 Ų buried · 10 hydrogen bonds · protein-protein
- D–E · 1142 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 1137 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1092 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 1WNC · Crystal structure of the SARS-CoV Spike protein fusion core · the same entry in another collection · chain B against B, TM-score 1.00
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.31
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against E, TM-score 0.31
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against E, TM-score 0.29
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against E, TM-score 0.29
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 P59594
- Elsewhere: RCSB PDB 1WNC · PDBe 1WNC · UniProt P59594
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