MolNFT v1 · #122288 · protein
1.9 ångström crystal structure of NS5 methyl transferase from dengue virus 1 in complex with S-adenosylmethionine and beta-D- fructopyranose.
5IKM: “1.9 ångström crystal structure of NS5 methyl transferase from dengue virus 1 in complex with…”. X-ray diffraction, 5 ligands (SAM, BDF, MLT), 1 pocket (best druggability 0.67). MolNFT v1 #122288 on GenesisL1: 3D structure, binding…
- PDB
- 5IKM
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NS5 methyl transferase
- UniProt
- I6XG39
- Ligands
- SAM, BDF, MLT, SO4, CL
- Pockets
- 1 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NS5 methyl transferase | protein | 259 | 38% helix, 15% strand | I6XG39 |
Ligands and binding sites
- SAM · S-adenosylmethionine · ligand · chains A
- BDF · beta-D-fructopyranose · ligand · chains A
- MLT · D-malate · ligand · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.67 | 0.77 | 61 | SO4, SAM |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 5IKM · 1.9 Angstrom Crystal Structure of NS5 Methyl Transferase from Dengue Virus 1 in Complex… · 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 I6XG39
- Elsewhere: RCSB PDB 5IKM · PDBe 5IKM · UniProt I6XG39
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