MolNFT v1 · #116952 · protein + RNA
Dengue virus full length NS5 complexed with viral cap 0-RNA and sah
5DTO: “Dengue virus full length NS5 complexed with viral cap 0-RNA and sah”. X-ray diffraction, 4 ligands (SAH, M7G, ZN), 12 pockets (best druggability 0.79). MolNFT v1 #116952 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DTO
- Type
- protein + RNA
- Length
- 856 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5; RNA (5'-R(P*AP*GP*UP*U)-3')
- UniProt
- A1XTB9
- Ligands
- SAH, M7G, ZN, MG
- Pockets
- 12 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5 | protein | 852 | 44% helix, 12% strand | A1XTB9 |
| B | RNA (5'-R(P*AP*GP*UP*U)-3') | rna | 4 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- M7G · 7N-methyl-8-hydroguanosine-5'-diphosphate · ligand · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.79 | 0.97 | 27 | empty |
| 2 | 261 | 0.72 | 0.87 | 35 | SAH |
| 3 | 634 | 0.70 | 0.78 | 63 | empty |
| 4 | 402 | 0.61 | 0.76 | 31 | empty |
| 5 | 210 | 0.56 | 0.79 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 506 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5DTO · Dengue virus full length NS5 complexed with viral Cap 0-RNA and SAH · 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 A1XTB9
- Elsewhere: RCSB PDB 5DTO · PDBe 5DTO · UniProt A1XTB9
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