Research workbench
Crystal structures of saccharomyces cerevisiae N-myristoyltransferase with bound myristoyl-CoA
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
- 2P6E
- Type
- protein
- Length
- 2,655 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
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 442 | 28% helix, 26% strand | P14743 |
| B, E | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 443 | 28% helix, 26% strand | P14743 |
| C | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 446 | 26% helix, 26% strand | P14743 |
| D | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 443 | 27% helix, 26% strand | P14743 |
| F | Glycylpeptide N-tetradecanoyltransferase (EC 2.3.1.97) | protein | 438 | 26% helix, 27% strand | P14743 |
Ligands and binding sites
- MYA · Tetradecanoyl-coa · 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 | 769 | 0.87 | 0.90 | 114 | MYA |
| 2 | 883 | 0.86 | 0.88 | 100 | MYA |
| 3 | 1186 | 0.86 | 0.86 | 128 | MYA |
| 4 | 523 | 0.85 | 0.90 | 68 | MYA |
| 5 | 501 | 0.84 | 0.90 | 60 | MYA |
Interfaces
7 interfaces between chains.
- A–C · 1125 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1063 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1061 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1042 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1032 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2P6E · 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 F 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 2P6E · PDBe 2P6E · UniProt P14743
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