MolNFT v1 · #47705 · protein
Crystal structures of saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors
2P6G · Glycylpeptide N-tetradecanoyltransferase: “Crystal structures of saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA and inhibitors”. X-ray diffraction, 2 ligands (MYA, 3LP), 20 pockets (best druggability 0.83).…
- PDB
- 2P6G
- Type
- protein
- Length
- 2,610 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, 3LP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 26% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 435 | 26% helix, 26% strand | P14743 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · ligand · 6 copies · chains A, B, C, D, E, F
- 3LP · 1-(cyclohexylamino)-3-(6-methyl-3,4-dihydro-1H-carbazol-9(2H)-yl)propan-2-ol · ligand · 2 copies · chains C, 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 | 943 | 0.83 | 0.84 | 134 | MYA |
| 2 | 1147 | 0.81 | 0.82 | 138 | MYA, 3LP |
| 3 | 1031 | 0.81 | 0.82 | 132 | MYA |
| 4 | 345 | 0.76 | 0.86 | 54 | empty |
| 5 | 328 | 0.74 | 0.85 | 47 | MYA |
Interfaces
7 interfaces between chains.
- D–F · 1008 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 1002 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 998 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 998 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 983 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2P6G · Crystal structures of Saccharomyces cerevisiae N-myristoyltransferase with bound… · the same entry in another collection · chain C against C, 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 2P6G · PDBe 2P6G · UniProt P14743
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