MolNFT v1 · #136690 · protein
Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium vivax in complex with inhibitor imp-0001088
5V0W: “Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium vivax in complex with inhibitor…”. X-ray diffraction, 4 ligands (MYA, KFK, SO4), 9 pockets (best druggability 0.82). MolNFT v1 #136690 on GenesisL1: 3D…
- PDB
- 5V0W
- Type
- protein
- Length
- 1,147 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
- A0A1G4HIY1
- Ligands
- MYA, KFK, SO4, CL
- 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 | 28% helix, 30% strand | A0A1G4HIY1 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 377 | 27% helix, 31% strand | A0A1G4HIY1 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 3 copies · chains A, B, C
- KFK · 1-[5-[3,4-bis(fluoranyl)-2-[2-(1,3,5-trimethylpyrazol-4-yl)ethoxy]phenyl]-1-methyl-indazol-3-yl]-~{N},~{N}-dimethyl-methanamine · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 11 copies · chains A, C, B
- CL · Chloride ion · ion · 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 | 786 | 0.82 | 0.85 | 93 | empty |
| 2 | 898 | 0.79 | 0.81 | 85 | MYA, KFK |
| 3 | 874 | 0.79 | 0.82 | 75 | MYA, KFK |
| 4 | 920 | 0.79 | 0.81 | 92 | MYA, KFK |
| 5 | 135 | 0.43 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 601 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 220 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5V0W · Crystal structure of glycylpeptide N-tetradecanoyltransferase from Plasmodium vivax in… · 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 A0A1G4HIY1
- Elsewhere: RCSB PDB 5V0W · PDBe 5V0W · UniProt A0A1G4HIY1
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