MolNFT v1 · #143503 · protein
Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium vivax in complex with inhibitor imp-0001173
6B1L: “Crystal structure of glycylpeptide N-tetradecanoyltransferase from plasmodium vivax in complex with inhibitor…”. X-ray diffraction, 2 ligands (MYA, CJ4), 7 pockets (best druggability 0.78). MolNFT v1 #143503 on GenesisL1: 3D…
- PDB
- 6B1L
- Type
- protein
- Length
- 693 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- A5K1A2
- Ligands
- MYA, CJ4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 378 | 28% helix, 30% strand | A5K1A2 |
| B | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 315 | 28% helix, 27% strand | A5K1A2 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · chains A
- CJ4 · 1-(5-fluoro-2-{methyl[3-(methylamino) propyl]amino}pyrimidin-4-yl)-N-[(imidazo[1,2-a]pyridin-3-yl)methyl]azetidine-3-carboxamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.78 | 0.80 | 85 | MYA, CJ4 |
| 2 | 709 | 0.74 | 0.80 | 78 | empty |
| 3 | 65 | 0.72 | 0.97 | 26 | empty |
| 4 | 648 | 0.68 | 0.77 | 64 | empty |
| 5 | 174 | 0.54 | 0.79 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 406 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6B1L · 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 A5K1A2
- Elsewhere: RCSB PDB 6B1L · PDBe 6B1L · UniProt A5K1A2
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