Research workbench
Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor (compound 34A)
Analyse Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4CAF
- Type
- protein
- Length
- 1,141 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
- 370, NHW, MG, NH4, CL, SO4
- Pockets
- 11 · best druggability 0.81
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 | 384 | 28% helix, 30% strand | A5K1A2 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 373 | 26% helix, 31% strand | A5K1A2 |
Ligands and binding sites
- 370 · 4-[(2-{5-[(3,5-dimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}-1-benzothiophen-3-yl)oxy]piperidine · 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
- NH4 · Ammonium ion · ion · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 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
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.81 | 0.83 | 99 | empty |
| 2 | 900 | 0.80 | 0.82 | 87 | 370, MG, NH4, NHW |
| 3 | 876 | 0.80 | 0.82 | 87 | 370, MG, NHW |
| 4 | 862 | 0.79 | 0.81 | 83 | 370, MG, NH4, NHW |
| 5 | 130 | 0.41 | 0.75 | 18 | empty |
Interfaces
2 interfaces between chains.
- A–B · 485 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 161 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4CAF · Plasmodium vivax N-myristoyltransferase in complex with a benzothiophene inhibitor… · 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 4CAF · PDBe 4CAF · UniProt A5K1A2
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