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Crystal structure of the infectious salmon anemia virus (isav) he viral receptor complex
Analyse Crystal structure of the infectious salmon anemia virus (isav) he viral… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T96
- Type
- protein
- Length
- 1,942 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- He protein
- UniProt
- Q9J0Y0
- Ligands
- 79J, MG
- Pockets
- 16 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | He protein | protein | 325 | 28% helix, 30% strand | Q9J0Y0 |
| B | He protein | protein | 330 | 28% helix, 29% strand | Q9J0Y0 |
| D | He protein | protein | 321 | 27% helix, 30% strand | Q9J0Y0 |
| F | He protein | protein | 316 | 26% helix, 30% strand | Q9J0Y0 |
Ligands and binding sites
- 79J · 4-O-acetyl-5-acetamido-3,5-dideoxy-L-glycero-alpha-D-galacto-non-2-ulopyranosonic acid · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- FMT · Formic acid · additive · 28 copies · chains A, B, C, F, D, E
- GOL · Glycerol · additive · 8 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1165 | 0.90 | 0.92 | 147 | GOL |
| 2 | 791 | 0.88 | 0.92 | 106 | FMT, GOL |
| 3 | 158 | 0.80 | 0.96 | 30 | FMT |
| 4 | 163 | 0.79 | 0.95 | 30 | FMT |
| 5 | 1095 | 0.78 | 0.80 | 140 | FMT |
Interfaces
8 interfaces between chains.
- B–C · 2191 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2187 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 2166 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 1922 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1894 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide (disulfide).
Compared structures
- 5T96 · Crystal structure of the infectious salmon anemia virus (ISAV) HE viral receptor complex · 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 Q9J0Y0
- Elsewhere: RCSB PDB 5T96 · PDBe 5T96 · UniProt Q9J0Y0
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