Research workbench
P.vivax NMT with aminomethylindazole and quinoline inhibitors bound
Analyse P.vivax NMT with aminomethylindazole and quinoline inhibitors bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5O4V
- Type
- protein
- Length
- 1,138 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.7
- Source
- Plasmodium vivax
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- A5K1A2
- Ligands
- NHW, 9K2, 9KZ, MG, SO4, CL
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · resolution 1.7 · 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 | 28% helix, 30% strand | A5K1A2 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 368 | 27% helix, 31% strand | A5K1A2 |
Ligands and binding sites
- NHW · 2-oxopentadecyl-CoA · ligand · 3 copies · chains A, B, C
- 9K2 · 1-[5-(4-fluoranyl-2-methyl-phenyl)-1~{H}-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine · ligand · 3 copies · chains A, B, C
- 9KZ · ethyl 2,4-dimethylquinoline-3-carboxylate · ligand · 3 copies · chains A, B, C
- MG · Magnesium ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.81 | 0.82 | 87 | NHW, 9K2, MG, 9KZ |
| 2 | 905 | 0.80 | 0.82 | 80 | NHW, 9K2, MG, 9KZ |
| 3 | 998 | 0.80 | 0.81 | 89 | NHW, 9K2, MG, 9KZ |
| 4 | 1185 | 0.79 | 0.81 | 99 | empty |
| 5 | 74 | 0.75 | 0.98 | 24 | DMS |
Interfaces
2 interfaces between chains.
- A–B · 428 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5O4V · P.VIVAX nmt with aminomethylindazole and quinoline inhibitors bound · 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 5O4V · PDBe 5O4V · UniProt A5K1A2
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