Research workbench
Dengue 3 NS5 protein with compound 29
Analyse Dengue 3 NS5 protein with compound 29 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJR
- Type
- protein
- Length
- 845 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- UniProt
- Q6DLV0
- Ligands
- SAH, 68E, ZN, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein | protein | 845 | 46% helix, 12% strand | Q6DLV0 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- 68E · 5-[5-(3-hydroxyprop-1-yn-1-yl)thiophen-2-yl]-4-methoxy-2-methyl-N-[(quinolin-8-yl)sulfonyl]benzamide · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 162 | 0.79 | 0.95 | 24 | EDO |
| 2 | 950 | 0.75 | 0.78 | 102 | empty |
| 3 | 455 | 0.64 | 0.77 | 42 | SAH |
| 4 | 257 | 0.59 | 0.79 | 41 | 68E |
| 5 | 328 | 0.55 | 0.75 | 31 | EDO, PEG |
Compared structures
- 5JJR · Dengue 3 NS5 protein with compound 29 · 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 Q6DLV0
- Elsewhere: RCSB PDB 5JJR · PDBe 5JJR · UniProt Q6DLV0
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