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Crystal structure of N-myristoyl transferase (nmt) G386E mutant from plasmodium vivax in complex with inhibitor imp-1002
Analyse Crystal structure of N-myristoyl transferase (nmt) G386E mutant from plasmodium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MB0
- Type
- protein
- Length
- 1,144 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
- YNC, JCY, CL, SO4
- Pockets
- 10 · 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 | 385 | 27% helix, 30% strand | A0A1G4HIY1 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 374 | 27% helix, 31% strand | A0A1G4HIY1 |
Ligands and binding sites
- YNC · Tetradec-13-ynoic acid - coa thioester · ligand · 3 copies · chains A, B, C
- JCY · 1-(5-{4-fluoro-2-[2-(1,3,5-trimethyl-1H-pyrazol-4-yl) ethoxy]phenyl}-1-methyl-1H-indazol-3-yl)-N,N-dimethylmethanamine · ligand · 3 copies · chains A, B, C
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.81 | 0.82 | 94 | empty |
| 2 | 999 | 0.80 | 0.81 | 89 | YNC, JCY |
| 3 | 879 | 0.80 | 0.82 | 76 | YNC, JCY |
| 4 | 849 | 0.80 | 0.83 | 77 | YNC, JCY |
| 5 | 52 | 0.71 | 0.98 | 22 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 397 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 76 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6MB0 · Crystal structure of N-myristoyl transferase (NMT) G386E mutant 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 6MB0 · PDBe 6MB0 · UniProt A0A1G4HIY1
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