MolNFT v1 · #41390 · protein + RNA
Dengue virus 4 NS3 helicase in complex with ssrna and ADP
2JLZ · Serine protease subunit NS3: “Dengue virus 4 NS3 helicase in complex with ssrna and ADP”. X-ray diffraction, 3 ligands (ADP, MN, CL), 12 pockets (best druggability 0.86). MolNFT v1 #41390 on GenesisL1: 3D structure, binding sites…
- PDB
- 2JLZ
- Type
- protein + RNA
- Length
- 916 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease subunit NS3; 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3'
- EC
- 3.4.21.91
- UniProt
- Q2YHF0
- Ligands
- ADP, MN, CL
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine protease subunit NS3 (EC 3.4.21.91) | protein | 451 | 32% helix, 18% strand | Q2YHF0 |
| C, D | 5'-R(*AP*GP*AP*CP*UP*AP*AP*CP*AP*AP*CP*U)-3' | rna | 7 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 840 | 0.86 | 0.89 | 104 | empty |
| 2 | 583 | 0.78 | 0.85 | 56 | empty |
| 3 | 250 | 0.78 | 0.91 | 41 | empty |
| 4 | 279 | 0.74 | 0.87 | 33 | empty |
| 5 | 102 | 0.52 | 0.83 | 20 | ADP, MN |
Interfaces
5 interfaces between chains.
- B–D · 1033 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–C · 1007 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 657 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 31 Ų buried · 0 hydrogen bonds · protein-nucleic
- A–D · 28 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 2JLZ · Dengue virus 4 NS3 helicase in complex with ssRNA and ADP · 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 Q2YHF0
- Elsewhere: RCSB PDB 2JLZ · PDBe 2JLZ · UniProt Q2YHF0
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