Research workbench
Crystal structure of yellow fever virus NS2B-NS3 protease domain
Analyse Crystal structure of yellow fever virus NS2B-NS3 protease domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6URV
- Type
- protein
- Length
- 770 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS2B; NS3 protease
- UniProt
- A0A2S1IYJ2, A0A346G7J0
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 5 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | NS2B | protein | 39 | 0% helix, 44% strand | A0A2S1IYJ2 |
| H, B | NS3 protease | protein | 154 | 3% helix, 49% strand | A0A346G7J0 |
| G, E | NS2B | protein | 38 | 0% helix, 45% strand | A0A2S1IYJ2 |
| F | NS3 protease | protein | 155 | 5% helix, 48% strand | A0A346G7J0 |
| D | NS3 protease | protein | 153 | 3% helix, 50% strand | A0A346G7J0 |
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.73 | 0.77 | 82 | empty |
| 2 | 1107 | 0.73 | 0.76 | 94 | empty |
| 3 | 224 | 0.53 | 0.77 | 31 | empty |
| 4 | 111 | 0.48 | 0.80 | 22 | empty |
| 5 | 110 | 0.44 | 0.77 | 18 | empty |
Interfaces
18 interfaces between chains.
- A–B · 2025 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 1959 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1899 Ų buried · 29 hydrogen bonds · protein-protein
- H–G · 1793 Ų buried · 27 hydrogen bonds · protein-protein
- F–D · 691 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6URV · Crystal structure of Yellow Fever Virus NS2B-NS3 protease domain · 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 A0A2S1IYJ2
- Every structure of UniProt A0A346G7J0
- Elsewhere: RCSB PDB 6URV · PDBe 6URV · UniProt A0A2S1IYJ2 · UniProt A0A346G7J0
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