Research workbench
Crystal structures of unlinked full length NS3 from dengue virus provide insights into dynamics of protease domain
Analyse Crystal structures of unlinked full length NS3 from dengue virus provide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YVU
- Type
- protein
- Length
- 694 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein; Pancreatic trypsin inhibitor
- UniProt
- F8TEL4, P00974
- Pockets
- 10 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 23% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Genome polyprotein | protein | 601 | 25% helix, 26% strand | F8TEL4 |
| A | Genome polyprotein | protein | 38 | 0% helix, 29% strand | F8TEL4 |
| I | Pancreatic trypsin inhibitor | protein | 55 | 13% helix, 25% strand | P00974 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1119 | 0.82 | 0.83 | 89 | empty |
| 2 | 269 | 0.67 | 0.83 | 40 | GOL |
| 3 | 53 | 0.51 | 0.88 | 22 | empty |
| 4 | 155 | 0.49 | 0.78 | 36 | empty |
| 5 | 87 | 0.48 | 0.82 | 17 | empty |
Interfaces
3 interfaces between chains.
- B–A · 1854 Ų buried · 28 hydrogen bonds · protein-protein
- B–I · 528 Ų buried · 10 hydrogen bonds · protein-protein
- A–I · 145 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 5YVU · Crystal structures of unlinked full length NS3 from Dengue virus provide insights into… · the same entry in another collection · chain B against B, TM-score 1.00
- P00974 · AlphaFold monomer V2.0 prediction for pancreatic trypsin inhibitor (P00974) · a predicted model of the same protein · chain I against A, TM-score 0.96
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 F8TEL4
- Every structure of UniProt P00974
- Elsewhere: RCSB PDB 5YVU · PDBe 5YVU · UniProt F8TEL4 · UniProt P00974
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