Research workbench
Crystal structure of dengue NS2B-NS3 protease after secondary cleavage
Analyse Crystal structure of dengue NS2B-NS3 protease after secondary cleavage in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7VMV
- Type
- protein
- Length
- 852 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Core protein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13
- UniProt
- A0A0M4C4I5, Q5I3B6
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 8 distinct chains · 2% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 54 | 0% helix, 50% strand | A0A0M4C4I5 |
| B | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 163 | 2% helix, 47% strand | Q5I3B6 |
| C | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 51 | 0% helix, 37% strand | A0A0M4C4I5 |
| D | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 153 | 3% helix, 49% strand | Q5I3B6 |
| E | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 52 | 0% helix, 50% strand | A0A0M4C4I5 |
| F | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 155 | 3% helix, 50% strand | Q5I3B6 |
| G | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 53 | 0% helix, 45% strand | A0A0M4C4I5 |
| H | Core protein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13) | protein | 171 | 2% helix, 44% strand | Q5I3B6 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.65 | 0.80 | 39 | empty |
| 2 | 257 | 0.54 | 0.76 | 30 | empty |
| 3 | 194 | 0.50 | 0.76 | 30 | empty |
| 4 | 185 | 0.47 | 0.75 | 27 | empty |
| 5 | 60 | 0.25 | 0.72 | 13 | empty |
Interfaces
12 interfaces between chains.
- A–B · 1704 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 1636 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 1623 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1557 Ų buried · 21 hydrogen bonds · protein-protein
- A–F · 481 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 7VMV · Crystal structure of Dengue NS2B-NS3 Protease after secondary cleavage · 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 A0A0M4C4I5
- Every structure of UniProt Q5I3B6
- Elsewhere: RCSB PDB 7VMV · PDBe 7VMV · UniProt A0A0M4C4I5 · UniProt Q5I3B6
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