Research workbench
Crystal structures of saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors
Analyse Crystal structures of saccharomyces cerevisiae N-myristoyltransferase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2P6F
- Type
- protein
- Length
- 2,615 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycylpeptide N-tetradecanoyltransferase
- EC
- 2.3.1.97
- UniProt
- P14743
- Ligands
- MYA, GN8
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 436 | 29% helix, 25% strand | P14743 |
| F | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 435 | 25% helix, 26% strand | P14743 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 6 copies · chains A, B, C, D, E, F
- GN8 · (Z)-3-benzyl-5-(2-hydroxy-3-nitrobenzylidene)-2-thioxothiazolidin-4-one · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1149 | 0.81 | 0.82 | 142 | MYA, GN8 |
| 2 | 677 | 0.79 | 0.84 | 114 | GN8 |
| 3 | 602 | 0.77 | 0.83 | 71 | MYA, GN8 |
| 4 | 609 | 0.76 | 0.82 | 71 | MYA, GN8 |
| 5 | 91 | 0.76 | 0.97 | 23 | empty |
Interfaces
7 interfaces between chains.
- D–F · 1008 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1005 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 990 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 983 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 972 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2P6F · Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound… · the same entry in another collection · chain F against F, TM-score 1.00
- P14743 · AlphaFold monomer V2.0 prediction for glycylpeptide N-tetradecanoyltransferase (P14743) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 P14743
- Elsewhere: RCSB PDB 2P6F · PDBe 2P6F · UniProt P14743
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