Research workbench
Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0 ångström resolution
Analyse Structural and biochemical analysis of human pathogenic astrovirus serine… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W5E
- Type
- protein
- Length
- 972 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative serine protease
- UniProt
- Q3ZN04
- Ligands
- CD, CL
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Putative serine protease | protein | 162 | 7% helix, 51% strand | Q3ZN04 |
Ligands and binding sites
- CD · Cadmium ion · metal · 18 copies · chains A, B, F, C, D, E
- CL · Chloride ion · ion · 28 copies · chains A, F, B, C, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1180 | 0.77 | 0.79 | 151 | CL |
| 2 | 239 | 0.53 | 0.76 | 29 | empty |
| 3 | 215 | 0.53 | 0.77 | 31 | empty |
| 4 | 169 | 0.52 | 0.79 | 24 | empty |
| 5 | 210 | 0.51 | 0.76 | 29 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1280 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1277 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1276 Ų buried · 26 hydrogen bonds · protein-protein
- C–E · 273 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 263 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2W5E · Structural and biochemical analysis of human pathogenic astrovirus serine protease at 2.0… · 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 Q3ZN04
- Elsewhere: RCSB PDB 2W5E · PDBe 2W5E · UniProt Q3ZN04
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