Research workbench
Crystal structure of the dengue virus methyltransferase bound to a 5'-capped octameric RNA
Analyse Crystal structure of the dengue virus methyltransferase bound to a 5'-capped… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XBM
- Type
- protein + RNA
- Length
- 1,051 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nonstructural protein NS5; 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3'
- UniProt
- C0LMU5
- Ligands
- SAH, G3A, SO4
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nonstructural protein NS5 | protein | 261 | 37% helix, 15% strand | C0LMU5 |
| B | Nonstructural protein NS5 | protein | 258 | 38% helix, 16% strand | C0LMU5 |
| C, D | Nonstructural protein NS5 | protein | 259 | 38% helix, 15% strand | C0LMU5 |
| E, F | 5'-(*G3AP*GP*AP*AP*CP*CP*UP*GP*A)-3' | rna | 7 | — | — |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- G3A · Guanosine-P3-adenosine-5',5'-triphosphate · ligand · 2 copies · chains B, E, A, F
- SO4 · Sulfate ion · ion · 12 copies · chains A, C, B, D
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 915 | 0.73 | 0.77 | 76 | SO4, SAH |
| 2 | 873 | 0.71 | 0.76 | 67 | SO4, SAH |
| 3 | 716 | 0.69 | 0.77 | 59 | G3A, SAH, GOL |
| 4 | 518 | 0.66 | 0.77 | 46 | SO4, SAH, GOL |
| 5 | 305 | 0.51 | 0.73 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–C · 809 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 655 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 404 Ų buried · 25 hydrogen bonds · nucleic-nucleic
- B–C · 280 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 277 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XBM · Crystal structure of the dengue virus methyltransferase bound to a 5'- capped octameric… · the same entry in another collection · chain F against F, 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 C0LMU5
- Elsewhere: RCSB PDB 2XBM · PDBe 2XBM · UniProt C0LMU5
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