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Crystal structure of N-myristoyl transferase (nmt) G386E mutant from plasmodium vivax
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
- 6MAY
- Type
- protein
- Length
- 1,136 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, CL, SO4
- Pockets
- 11 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 382 | 27% helix, 30% strand | A0A1G4HIY1 |
| B | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 370 | 27% helix, 31% strand | A0A1G4HIY1 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 384 | 29% helix, 30% strand | A0A1G4HIY1 |
Ligands and binding sites
- YNC · Tetradec-13-ynoic acid - coa thioester · 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, C
- EDO · 1,2-ethanediol · additive · 4 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 | 1192 | 0.79 | 0.80 | 99 | empty |
| 2 | 824 | 0.78 | 0.81 | 81 | YNC |
| 3 | 720 | 0.77 | 0.81 | 81 | YNC |
| 4 | 714 | 0.76 | 0.81 | 66 | YNC |
| 5 | 132 | 0.41 | 0.75 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 429 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6MAY · Crystal structure of N-myristoyl transferase (NMT) G386E mutant from Plasmodium vivax · 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 6MAY · PDBe 6MAY · UniProt A0A1G4HIY1
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