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A structure-based mechanism of SARS virus membrane fusion
Analyse A structure-based mechanism of SARS virus membrane fusion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1ZV8
- Type
- protein
- Length
- 477 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E2 glycoprotein
- UniProt
- P59594
- Ligands
- NA, ZN
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 8 distinct chains · 76% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, I | E2 glycoprotein | protein | 49 | 96% helix, 0% strand | P59594 |
| B | E2 glycoprotein | protein | 27 | 63% helix, 0% strand | P59594 |
| C | E2 glycoprotein | protein | 46 | 96% helix, 0% strand | P59594 |
| D | E2 glycoprotein | protein | 29 | 59% helix, 0% strand | P59594 |
| F, J | E2 glycoprotein | protein | 30 | 57% helix, 0% strand | P59594 |
| G, K | E2 glycoprotein | protein | 50 | 96% helix, 0% strand | P59594 |
| H | E2 glycoprotein | protein | 34 | 50% helix, 0% strand | P59594 |
| L | E2 glycoprotein | protein | 34 | 59% helix, 0% strand | P59594 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, G, L, H, F, J, K
- ZN · Zinc ion · metal · 2 copies · chains G, H
- CAC · Cacodylate ion · additive · chains G, H
- ACT · Acetate ion · additive · chains G, H
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 | 53 | 0.73 | 0.99 | 16 | empty |
| 2 | 54 | 0.73 | 0.99 | 17 | empty |
| 3 | 365 | 0.56 | 0.75 | 40 | empty |
| 4 | 82 | 0.38 | 0.77 | 14 | empty |
| 5 | 71 | 0.31 | 0.74 | 13 | empty |
Interfaces
22 interfaces between chains.
- G–L · 1040 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1032 Ų buried · 19 hydrogen bonds · protein-protein
- H–I · 1022 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 981 Ų buried · 15 hydrogen bonds · protein-protein
- K–L · 978 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1ZV8 · A structure-based mechanism of SARS virus membrane fusion · the same entry in another collection · chain K against K, 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 P59594
- Elsewhere: RCSB PDB 1ZV8 · PDBe 1ZV8 · UniProt P59594
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