Research workbench
Dengue virus non structural protein 5
Analyse Dengue virus non structural protein 5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ZQK
- Type
- protein
- Length
- 1,749 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non structural protein 5
- UniProt
- H9M652
- Ligands
- SAM, ZN, MG
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non structural protein 5 | protein | 874 | 43% helix, 13% strand | H9M652 |
| B | Non structural protein 5 | protein | 875 | 44% helix, 13% strand | H9M652 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.78 | 0.81 | 74 | GOL |
| 2 | 1079 | 0.78 | 0.79 | 99 | GOL |
| 3 | 841 | 0.72 | 0.77 | 66 | SAM |
| 4 | 833 | 0.72 | 0.77 | 75 | SAM |
| 5 | 239 | 0.53 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1079 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5ZQK · Dengue Virus Non Structural Protein 5 · 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 H9M652
- Elsewhere: RCSB PDB 5ZQK · PDBe 5ZQK · UniProt H9M652
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