Research workbench
Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 19)
Analyse Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UFX
- Type
- protein
- Length
- 1,142 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- A5K1A2
- Ligands
- 80O, NHW, MG, CL, SO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 385 | 27% helix, 30% strand | A5K1A2 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 372 | 26% helix, 31% strand | A5K1A2 |
Ligands and binding sites
- 80O · N-[2-(3-methoxyphenyl)ethanimidoyl]-2-piperidin-4-yloxy-pyridine-3-carboxamide · ligand · 3 copies · chains A, B, C
- NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 6 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.82 | 0.85 | 97 | CL |
| 2 | 913 | 0.81 | 0.82 | 78 | 80O, NHW, MG |
| 3 | 891 | 0.80 | 0.82 | 80 | 80O, NHW, MG |
| 4 | 889 | 0.79 | 0.82 | 76 | 80O, NHW, MG |
| 5 | 64 | 0.48 | 0.84 | 22 | empty |
Interfaces
2 interfaces between chains.
- A–B · 796 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 230 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4UFX · Plasmodium vivax N-myristoyltransferase in complex with a pyridyl inhibitor (compound 19) · 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 A5K1A2
- Elsewhere: RCSB PDB 4UFX · PDBe 4UFX · UniProt A5K1A2
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