Research workbench
Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and fragment 2A4
Analyse Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and fragment 2A4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CTK
- Type
- protein
- Length
- 512 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polyprotein
- EC
- 2.1.1.56, 2.1.1.57
- UniProt
- A9LIE0
- Ligands
- SAM, SVN, NA
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Polyprotein (EC 2.1.1.56, 2.1.1.57) | protein | 256 | 37% helix, 16% strand | A9LIE0 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C
- SVN · thieno[2,3-b]pyrazin-7-amine · ligand · 2 copies · chains A
- NA · Sodium ion · metal · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 568 | 0.66 | 0.77 | 56 | SAM |
| 2 | 509 | 0.66 | 0.77 | 48 | SAM |
| 3 | 58 | 0.47 | 0.85 | 22 | empty |
| 4 | 64 | 0.39 | 0.80 | 18 | empty |
| 5 | 98 | 0.34 | 0.73 | 22 | empty |
Interfaces
1 interface between chains.
- A–C · 516 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4CTK · Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and fragment 2A4 · the same entry in another collection · chain C against C, 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 A9LIE0
- Elsewhere: RCSB PDB 4CTK · PDBe 4CTK · UniProt A9LIE0
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