MolNFT v1 · #134625 · protein
Crystal structure of the infectious salmon anemia virus (isav) hemagglutinin-esterase protein
5T9Y · He protein: “Crystal structure of the infectious salmon anemia virus (isav) hemagglutinin-esterase protein”. X-ray diffraction, 1 ligand (MG), 8 pockets (best druggability 0.90). MolNFT v1 #134625 on GenesisL1: 3D structure, binding…
- PDB
- 5T9Y
- Type
- protein
- Length
- 959 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- He protein
- UniProt
- Q9J0Y0
- Ligands
- MG
- Pockets
- 8 · best druggability 0.90
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | He protein | protein | 321 | 27% helix, 30% strand | Q9J0Y0 |
| B, C | He protein | protein | 319 | 26% helix, 30% strand | Q9J0Y0 |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- FMT · Formic acid · additive · 23 copies · chains A, B, C
- GOL · Glycerol · additive · 3 copies · chains A, B
- 15P · Polyethylene glycol (N=34) · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.90 | 0.91 | 152 | GOL, FMT |
| 2 | 163 | 0.78 | 0.95 | 29 | FMT |
| 3 | 54 | 0.57 | 0.91 | 18 | empty |
| 4 | 91 | 0.47 | 0.81 | 24 | empty |
| 5 | 107 | 0.45 | 0.79 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2037 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 2018 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 1977 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 5T9Y · Crystal structure of the infectious salmon anemia virus (ISAV) hemagglutinin-esterase… · 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 5T9Y · PDBe 5T9Y · UniProt Q9J0Y0
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