Research workbench
Crystal structure of a GII.4 norovirus hov protease
Analyse Crystal structure of a GII.4 norovirus hov protease in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NIR
- Type
- protein
- Length
- 699 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hov protease; Hov protease fragment
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 7% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hov protease | protein | 169 | 9% helix, 51% strand | — |
| B | Hov protease | protein | 170 | 6% helix, 49% strand | — |
| C | Hov protease | protein | 180 | 7% helix, 47% strand | — |
| D | Hov protease | protein | 174 | 7% helix, 50% strand | — |
| X | Hov protease fragment | protein | 6 | 0% helix, 17% strand | — |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.81 | 0.83 | 111 | empty |
| 2 | 179 | 0.54 | 0.79 | 27 | empty |
| 3 | 65 | 0.41 | 0.81 | 21 | empty |
| 4 | 91 | 0.38 | 0.76 | 20 | empty |
| 5 | 56 | 0.31 | 0.76 | 16 | empty |
Interfaces
7 interfaces between chains.
- A–D · 963 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 919 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 634 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 260 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 225 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6NIR · Crystal structure of a GII.4 norovirus HOV protease · 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
- Elsewhere: RCSB PDB 6NIR · PDBe 6NIR
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