MolNFT v1 · #10673 · protein
Crystal structure of candida albicans N-myristoyltransferase with myristoyl-CoA and peptidic inhibitor
1IYK · Myristoyl-COA:PROTEIN N-myristoyltransferase: “Crystal structure of candida albicans N-myristoyltransferase with myristoyl-CoA and peptidic inhibitor”. X-ray diffraction, 2 ligands (MYA, MIM), 11 pockets (best druggability 0.75).…
- PDB
- 1IYK
- Type
- protein
- Length
- 784 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myristoyl-COA:PROTEIN N-myristoyltransferase
- EC
- 2.3.1.97
- UniProt
- P30418
- Ligands
- MYA, MIM
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Myristoyl-COA:PROTEIN N-myristoyltransferase (EC 2.3.1.97) | protein | 392 | 27% helix, 30% strand | P30418 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 2 copies · chains A, B
- MIM · [cyclohexylethyl]-[[[[4-[2-methyl-1-imidazolyl-butyl]phenyl]acetyl]-seryl]-lysinyl]-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.75 | 0.80 | 93 | MYA, MIM |
| 2 | 739 | 0.74 | 0.79 | 83 | MYA, MIM |
| 3 | 102 | 0.41 | 0.77 | 20 | empty |
| 4 | 76 | 0.38 | 0.78 | 15 | empty |
| 5 | 76 | 0.37 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2034 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1IYK · Crystal structure of candida albicans N-myristoyltransferase with myristoyl-COA and… · the same entry in another collection · chain A against A, TM-score 1.00
- P30418 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase (P30418) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P30418
- Elsewhere: RCSB PDB 1IYK · PDBe 1IYK · UniProt P30418
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