MolNFT v1 · #117491 · protein
Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and molecule BF174
5E9Q · Genome polyprotein: “Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and molecule BF174”. X-ray diffraction, 2 ligands (SAM, 5KY), 4 pockets (best druggability 0.68). MolNFT v1 #117491 on GenesisL1: 3D structure…
- PDB
- 5E9Q
- Type
- protein
- Length
- 511 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Genome polyprotein
- EC
- 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48
- UniProt
- P27915
- Ligands
- SAM, 5KY
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 255 | 37% helix, 15% strand | P27915 |
| C | Genome polyprotein (EC 3.4.21.91, 3.6.1.15, 3.6.4.13, 2.1.1.56, 2.1.1.57, 2.7.7.48) | protein | 256 | 38% helix, 16% strand | P27915 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · 2 copies · chains A, C
- 5KY · 2-({[2-amino-4-(trifluoromethyl)phenyl]carbamoyl}amino)-4-methylbenzoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.68 | 0.78 | 58 | SAM |
| 2 | 548 | 0.67 | 0.77 | 49 | SAM |
| 3 | 58 | 0.41 | 0.81 | 18 | empty |
| 4 | 77 | 0.30 | 0.72 | 21 | empty |
Interfaces
1 interface between chains.
- A–C · 547 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5E9Q · Dengue 3 NS5 methyltransferase bound to S-adenosyl methionine and molecule BF174 · 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 P27915
- Elsewhere: RCSB PDB 5E9Q · PDBe 5E9Q · UniProt P27915
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