MolNFT v1 · #141088 · protein
Crystal structures of unlinked full length NS3 from dengue virus provide insights into dynamics of protease domain
5YVU · Genome polyprotein: “Crystal structures of unlinked full length NS3 from dengue virus provide insights into dynamics of protease…”. X-ray diffraction, 10 pockets (best druggability 0.82). MolNFT v1 #141088 on GenesisL1: 3D…
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.