MolNFT v1 · #10674 · protein
Crystal structure of candida albicans N-myristoyltransferase with non- peptidic inhibitor
1IYL · Myristoyl-COA:PROTEIN N-myristoyltransferase: “Crystal structure of candida albicans N-myristoyltransferase with non- peptidic inhibitor”. X-ray diffraction, 1 ligand (R64), 20 pockets (best druggability 0.78). MolNFT v1 #10674 on…
- PDB
- 1IYL
- Type
- protein
- Length
- 1,525 residues
- Chains
- 4
- 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
- R64
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Myristoyl-COA:PROTEIN N-myristoyltransferase (EC 2.3.1.97) | protein | 384 | 26% helix, 28% strand | P30418 |
| B, D | Myristoyl-COA:PROTEIN N-myristoyltransferase (EC 2.3.1.97) | protein | 380 | 27% helix, 27% strand | P30418 |
| C | Myristoyl-COA:PROTEIN N-myristoyltransferase (EC 2.3.1.97) | protein | 381 | 25% helix, 27% strand | P30418 |
Ligands and binding sites
- R64 · (1-methyl-1H-imidazol-2-yl)-(3-methyl-4-{3-[(pyridin-3-ylmethyl)-amino]-propoxy}-benzofuran-2-yl)-methanone · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 671 | 0.78 | 0.83 | 63 | R64 |
| 2 | 628 | 0.78 | 0.83 | 67 | R64 |
| 3 | 780 | 0.78 | 0.81 | 75 | R64 |
| 4 | 683 | 0.76 | 0.81 | 80 | empty |
| 5 | 61 | 0.72 | 0.97 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1218 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1182 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1IYL · Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor · 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 C against A, TM-score 0.97
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 1IYL · PDBe 1IYL · UniProt P30418
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