MolNFT v1 · #139322 · protein + RNA
Dengue virus 4 NS3 helicase in complex with ssrna SLA12
5XC6: “Dengue virus 4 NS3 helicase in complex with ssrna SLA12”. X-ray diffraction, 1 ligand (PO4), 13 pockets (best druggability 0.86). MolNFT v1 #139322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XC6
- Type
- protein + RNA
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS3 helicase; RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3')
- UniProt
- M9P7S0
- Ligands
- PO4
- Pockets
- 13 · 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 | NS3 helicase | protein | 451 | 32% helix, 18% strand | M9P7S0 |
| C, D | RNA (5'-R(*AP*GP*UP*UP*GP*UP*UP*AP*GP*UP*CP*U)-3') | rna | 5 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.86 | 0.90 | 83 | empty |
| 2 | 568 | 0.85 | 0.91 | 71 | empty |
| 3 | 520 | 0.76 | 0.83 | 35 | empty |
| 4 | 205 | 0.60 | 0.81 | 34 | PO4 |
| 5 | 121 | 0.57 | 0.85 | 28 | PO4 |
Interfaces
4 interfaces between chains.
- B–D · 823 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 814 Ų buried · 14 hydrogen bonds · protein-nucleic
- A–B · 544 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 15 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 5XC6 · Dengue Virus 4 NS3 Helicase in complex with SSRNA SLA12 · 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 M9P7S0
- Elsewhere: RCSB PDB 5XC6 · PDBe 5XC6 · UniProt M9P7S0
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